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** **

 

** **

**UNITED STATES**

**SECURITIES AND EXCHANGE COMMISSION**

**Washington, D.C. 20549**

 

**Form 10-K/A**

**(Amendment No.1)**

 

**ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(D)**

** OF THE SECURITIES EXCHANGE ACT OF 1934**

**FOR THE FISCAL YEAR ENDED SEPTEMBER 30, 2012**

 

**COMMISSION FILE NUMBER: 001-35608**

 

 

**Natural Grocers by Vitamin Cottage, Inc.**

(Exact name of registrant as specified in its charter)

 

| **Delaware**                    |   | **45-5034161**         |
|---------------------------------|--------|------------------------|
| (State or other jurisdiction of |   | (I.R.S. Employer       |
| incorporation or organization)  |   | Identification Number) |

 

**12612 West Alameda Parkway**

**Lakewood, Colorado 80228**

(Address of principal executive offices)

 

**(303) 986-4600**

(Registrants telephone number, including area code)

 

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes o No x

 

Indicate by checkmark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes o No x

 

Indicate by checkmark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.  Yes x No o

 

Indicate by checkmark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes x No o

 

Indicate by checkmark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. o

 

Indicate by checkmark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company (as defined in Rule 12b-2 of the Exchange Act).

 

| Large accelerated filer o               |   | Accelerated filer o         |
|----------------------------------------------|--------|----------------------------------|
| Non —accelerated filer x                |   | Smaller Reporting Company o |
| (Do not check if a smaller reorting company) |   |                             |

 

Indicate by checkmark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes o  No x

 

The aggregate market value of all common stock held by non-affiliates of the registrant as of July 25, 2012 was $127,571,426.  The registrant was a privately held company on March 30, 2012, which is the last business day of its second fiscal quarter.  As a result, the registrant is disclosing this information as of July 25, 2012, which was the initial trading date of the registrant’s common stock on the New York Stock Exchange.  The number of shares of the registrant’s common stock outstanding as of December 12, 2012 was 22,372,184.

 

**DOCUMENTS INCORPORATED BY REFERENCE**

 

The information required by Part III of this report, to the extent not set forth herein, is incorporated by reference from the Registrant’s definitive Proxy Statement for the 2013 Annual Meeting of the Stockholders, which will be filed with the Securities and Exchange Commission not later than 120 days after September 30, 2012.

 

 

 

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**EXPLANATORY NOTE**

 

This Amendment No. 1 on Form 10-K/A (this “Amendment”) to the Annual Report on Form 10-K of Natural Grocers by Vitamin Cottage, Inc. (the “Company”) for the fiscal year ended September 30, 2012, initially filed with the Securities and Exchange Commission (the “SEC”) on December 13, 2012 (the “Original Filing”), is being filed to correct two administrative errors in the Original Filing. Specifically, the Original Filing inadvertently (i) did not include a conformed signature on the report of independent registered accounting firm from KPMG LLP (“KPMG”) included in Item 8 and (ii) did not include a conformed signature on the consent from KPMG in Exhibit 23.1.

 

In addition, pursuant to the rules of the SEC, “Item 8. Financial Statements and Supplementary Data” is being filed in its entirety in this Amendment. The only change in Item 8 from the Original Filing has been to add the conformed signature to the report of independent registered accounting firm.

 

Finally, consistent with the rules of the SEC, the certifications of the Company’s principal executive officers and principal financial and accounting officer as of the date of this Amendment are attached as exhibits to this Amendment. The only change in these certifications is their date.

 

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**PART II**

 

**Item 8.  Financial Statements and Supplementary Data.**

 

**Natural Grocers by Vitamin Cottage, Inc.**

**Index to Consolidated Financial Statements**

 
| ** **                                                                                                                   | ** ** | **Page   Number** |
|------------------------------------------------------------------------------------------------------------------------------|------------|-------------------|
| Report   of Independent Registered Public Accounting Firm                                                                    |       | 3                 |
| Consolidated Balance Sheets as of September 30,   2012 and 2011                                                         |       | 4                 |
| Consolidated Statements of Income for the years ended   September 30, 2012, 2011 and 2010                               |       | 5                 |
| Consolidated Statements of Cash Flows for the years   ended September 30, 2012, 2011 and 2010                           |       | 6                 |
| Consolidated Statements of Changes in Stockholders’   Equity for the years ended September 30, 2012, 2011 and 2010 |       | 7                 |
| Notes to Consolidated Financial Statements                                                                                   |       | 8                 |

 

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**Report of Independent Registered Public Accounting Firm**

 

The Board of Directors and Stockholders

Natural Grocers by Vitamin Cottage, Inc.:

 

We have audited the accompanying consolidated balance sheets of Natural Grocers by Vitamin Cottage, Inc. and subsidiaries (the Company) as of September 30, 2012 and 2011, and the related consolidated statements of income, changes in stockholders’ equity and comprehensive income, and cash flows for each of the years in the three-year period ended September 30, 2012. These consolidated financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on these consolidated financial statements based on our audits.

 

We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement. An audit includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements. An audit also includes assessing the accounting principles used and significant estimates made by management, as well as evaluating the overall financial statement presentation. We believe that our audits provide a reasonable basis for our opinion.

 

In our opinion, the consolidated financial statements referred to above present fairly, in all material respects, the financial position of Natural Grocers by Vitamin Cottage, Inc. and subsidiaries as of September 30, 2012 and 2011, and the results of their operations and their cash flows for each of the years in the three-year period ended September 30, 2012, in conformity with U.S. generally accepted accounting principles.

 
|                | /s/   KPMG LLP |
|---------------------|----------------|
|                |           |
| Denver,   Colorado  |           |
| December   12, 2012 |           |

 

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**NATURAL GROCERS BY VITAMIN COTTAGE, INC.**

 

**Consolidated Balance Sheets**

 
| ** **                                                                                                                                                                                                                 | ** ** | **September 30,** | ** **        |
|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|------------------------|-------------------|
| ** **                                                                                                                                                                                                                 | ** ** | **2012**               | ** **        | **2011** | ** ** |
| **Assets**                                                                                                                                                                                                                 |       |                   |              |   |   |
| Current assets:                                                                                                                                                                                                            |       |                   |              |   |   |
| Cash and cash equivalents                                                                                                                                                                                                  |       | $                      |  17,290,948  |   | 377,549 |   |
| Short term investments — available-for-sale   securities                                                                                                                                                              |       | 777,445                |              | — |   |
| Accounts receivable, net                                                                                                                                                                                                   |       | 1,755,142              |              | 1,027,141 |   |
| Accounts receivable—leasehold incentives                                                                                                                                                                              |       | 100,274                |              | 1,111,475 |   |
| Merchandise inventory                                                                                                                                                                                                      |       | 37,543,861             |              | 29,820,321 |   |
| Prepaid expenses                                                                                                                                                                                                           |       | 596,090                |              | 455,126 |   |
| Income tax receivable                                                                                                                                                                                                      |       | —                 |              | 1,701,917 |   |
| Deferred income tax assets                                                                                                                                                                                                 |       | 842,963                |              | 583,668 |   |
| Total current assets                                                                                                                                                                                                       |       | 58,906,723             |              | 35,077,197 |   |
| Property and equipment, net                                                                                                                                                                                                |       | 64,602,743             |              | 41,737,234 |   |
| Other assets:                                                                                                                                                                                                              |       |                   |              |   |   |
| Long-term investments — available-for-sale   securities                                                                                                                                                               |       | 973,729                |              | — |   |
| Deposits and other assets                                                                                                                                                                                                  |       | 196,365                |              | 167,558 |   |
| Goodwill                                                                                                                                                                                                                   |       | 511,029                |              | 511,029 |   |
| Deferred financing costs, net                                                                                                                                                                                              |       | 54,643                 |              | 88,631 |   |
| Other intangibles, net                                                                                                                                                                                                     |       | 416,464                |              | 490,301 |   |
| Split-dollar life insurance premiums                                                                                                                                                                                       |       | —                 |              | 577,861 |   |
| Notes receivable—related party, long-term                                                                                                                                                                             |       | —                 |              | 265,572 |   |
| Total other assets                                                                                                                                                                                                         |       | 2,152,230              |              | 2,100,952 |   |
| Total assets                                                                                                                                                                                                               |       | $                      |  125,661,696 |   | 78,915,383 |   |
| **Liabilities   and Stockholders’ Equity**                                                                                                                                                                            |       |                   |              |   |   |
| Current liabilities:                                                                                                                                                                                                       |       |                   |              |   |   |
| Accounts payable                                                                                                                                                                                                           |       | $                      |  26,031,756  |   | 16,087,882 |   |
| Accrued expenses                                                                                                                                                                                                           |       | 7,783,430              |              | 5,785,499 |   |
| Long-term debt, current portion                                                                                                                                                                                            |       | —                 |              | 500,000 |   |
| Revolving credit facility                                                                                                                                                                                                  |       | —                 |              | 11,036,324 |   |
| Notes payable—related party, current portion                                                                                                                                                                          |       | 260,187                |              | 562,271 |   |
| Capital lease finance obligation, current portion                                                                                                                                                                          |       | 11,884                 |              | — |   |
| Total current liabilities                                                                                                                                                                                                  |       | 34,087,257             |              | 33,971,976 |   |
| Long-term liabilities:                                                                                                                                                                                                     |       |                   |              |   |   |
| Capital lease finance obligation, net of current   portion                                                                                                                                                                 |       | 4,168,700              |              | — |   |
| Capital lease finance obligation for assets under   construction                                                                                                                                                           |       | 1,345,258              |              | — |   |
| Deferred income tax liabilities                                                                                                                                                                                            |       | 4,143,351              |              | 4,947,870 |   |
| Deferred rent                                                                                                                                                                                                              |       | 3,618,233              |              | 2,845,292 |   |
| Leasehold incentives                                                                                                                                                                                                       |       | 5,327,408              |              | 4,879,432 |   |
| Long-term debt, net of current portion                                                                                                                                                                                     |       | —                 |              | 15,700,000 |   |
| Notes payable—related party, net of current   portion                                                                                                                                                                 |       | 22,312                 |              | 643,834 |   |
| Total long-term liabilities                                                                                                                                                                                                |       | 18,625,262             |              | 29,016,428 |   |
| Total liabilities                                                                                                                                                                                                          |       | 52,712,519             |              | 62,988,404 |   |
| Commitments (Notes 13 and 21)                                                                                                                                                                                         |       |                   |              |   |   |
| Stockholders’ equity:                                                                                                                                                                                                 |       |                   |              |   |   |
| Common stock, $0.001 par value. Authorized   50,000,000 shares, 22,372,184 issued and outstanding at 2012, none issued and   outstanding at 2011                                                                           |       | 22,372                 |              | — |   |
| Common stock Vitamin Cottage Natural Food   Markets, Inc., Class A, voting, no par value. None issued and   outstanding at 2012. Authorized 1,000 shares, issued and outstanding at 2011                         |       | —                 |              | 1,679 |   |
| Common stock Vitamin Cottage Natural Food   Markets, Inc., Class B, nonvoting, no par value. None issued and   outstanding at 2012. Authorized 1,000,000 shares, 625,112 shares issued and   outstanding at 2011 |       | —                 |              | 792,676 |   |
| Additional paid in capital                                                                                                                                                                                                 |       | 52,675,925             |              | — |   |
| Accumulated other comprehensive loss                                                                                                                                                                                       |       | (3,696                 | )                 | — |   |
| Retained earnings                                                                                                                                                                                                          |       | 20,254,576             |              | 13,605,776 |   |
| Total Natural Grocers by Vitamin   Cottage, Inc. equity                                                                                                                                                               |       | 72,949,177             |              | 14,400,131 |   |
| Noncontrolling interest                                                                                                                                                                                                    |       | —                 |              | 1,526,848 |   |
| Total stockholders’ equity                                                                                                                                                                                            |       | 72,949,177             |              | 15,926,979 |   |
| Total liabilities and stockholders’ equity                                                                                                                                                                            |       | $                      |  125,661,696 |   | 78,915,383 |   |

 

See accompanying notes to consolidated financial statements.

 

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**NATURAL GROCERS BY VITAMIN COTTAGE, INC.**

 

**Consolidated Statements of Income**

 
| ** **                                                                                                                                                                                              | ** ** | **Year ended September 30,** | ** **        |
|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|---------------------------------------------|-------------------|
| ** **                                                                                                                                                                                              | ** ** | **2012**                                    | ** **        | **2011** | ** ** | **2010** | ** ** |
| Net sales                                                                                                                                                                                               |       | $                                           |  336,385,372 |   | 264,544,046 |   | 226,910,054 |   |
| Cost of goods sold and occupancy costs (includes   depreciation expense of $435,347, $449,208 and $435,148, respectively,   exclusive of additional depreciation and amortization expense listed below) |       | 237,328,764                                 |              | 187,162,252 |   | 159,797,435 |   |
| Gross profit                                                                                                                                                                                            |       | 99,056,608                                  |              | 77,381,794 |   | 67,112,619 |   |
| Store expenses (includes depreciation and   amortization expense of $8,710,116, $6,402,417 and $4,292,628, respectively)                                                                                |       | 72,157,131                                  |              | 57,609,690 |   | 47,162,167 |   |
| Administrative expenses (includes depreciation and   amortization expense of $802,780, $839,153 and $782,404, respectively)                                                                             |       | 12,732,100                                  |              | 10,396,891 |   | 9,630,646 |   |
| Pre-opening and relocation expenses                                                                                                                                                                     |       | 2,173,181                                   |              | 1,964,186 |   | 1,292,965 |   |
|                                                                                                                                                                                                    |       | 87,062,412                                  |              | 69,970,767 |   | 58,085,778 |   |
| Operating income                                                                                                                                                                                        |       | 11,994,196                                  |              | 7,411,027 |   | 9,026,841 |   |
| Other income (expense):                                                                                                                                                                                 |       |                                        |              |   |   |   |   |
| Dividends and interest income                                                                                                                                                                           |       | 6,096                                       |              | 10,077 |   | 6,721 |   |
| Interest expense                                                                                                                                                                                        |       | (568,501                                    | )                 | (669,125 | ) | (967,551 | ) |
| Other income (expense), net                                                                                                                                                                             |       | —                                      |              | 24,707 |   | (3,671 | ) |
| Total other expense                                                                                                                                                                                     |       | (562,405                                    | )                 | (634,341 | ) | (964,501 | ) |
| Income before income taxes                                                                                                                                                                              |       | 11,431,791                                  |              | 6,776,686 |   | 8,062,340 |   |
| Provision for income taxes                                                                                                                                                                              |       | (3,955,219                                  | )                 | (2,166,800 | ) | (2,465,772 | ) |
| Net income                                                                                                                                                                                              |       | 7,476,572                                   |              | 4,609,886 |   | 5,596,568 |   |
| Net income attributable to noncontrolling interest                                                                                                                                                      |       | (827,772                                    | )                 | (1,106,075 | ) | (1,188,605 | ) |
| Net income attributable to Natural Grocers by   Vitamin Cottage, Inc.                                                                                                                              |       | $                                           |  6,648,800   |   | 3,503,811 |   | 4,407,963 |   |
|                                                                                                                                                                                                    |       |                                        |              |   |   |   |   |
| Net income attributable to Natural Grocers by   Vitamin Cottage, Inc. per common share:                                                                                                            |       |                                        |              |   |   |   |   |
| Basic                                                                                                                                                                                                   |       | $                                           |  0.30        |   | 0.16 |   | 0.20 |   |
| Diluted                                                                                                                                                                                                 |       | $                                           |  0.30        |   | 0.16 |   | 0.20 |   |
| Weighted average common shares outstanding:                                                                                                                                                             |       |                                        |              |   |   |   |   |
| Basic                                                                                                                                                                                                   |       | 22,372,184                                  |              | 22,372,184 |   | 22,372,184 |   |
| Diluted                                                                                                                                                                                                 |       | 22,463,093                                  |              | 22,461,405 |   | 22,461,405 |   |

 

See accompanying notes to consolidated financial statements.

 

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**NATURAL GROCERS BY VITAMIN COTTAGE, INC.**

 

**Consolidated Statements of Cash Flows**

 
| ** **                                                                                          | ** ** | **Year ended September 30,** | ** **       |
|-----------------------------------------------------------------------------------------------------|------------|---------------------------------------------|------------------|
| ** **                                                                                          | ** ** | **2012**                                    | ** **       | **2011** | ** ** | **2010** | ** ** |
| Operating activities:                                                                               |       |                                        |             |   |   |   |   |
| Net income                                                                                          |       | $                                           |  7,476,572  |   | 4,609,886 |   | 5,596,568 |   |
| Adjustments to reconcile net income to net cash   provided by operating activities:                 |       |                                        |             |   |   |   |   |
| Depreciation and amortization                                                                       |       | 9,948,243                                   |             | 7,690,778 |   | 5,510,180 |   |
| Loss (gain) on disposal of property and equipment                                                   |       | 300,676                                     |             | (24,707 | ) | 8,021 |   |
| Stock-based compensation (excluding cash portion   of restricted stock award paid of $334,579)      |       | 779,979                                     |             | — |   | — |   |
| Excess tax benefit from stock-based compensation                                                    |       | (620,138                                    | )                | — |   | — |   |
| Deferred income tax expense                                                                         |       | 2,673,248                                   |             | 3,937,798 |   | 596,108 |   |
| Non-cash interest expense                                                                           |       | 38,036                                      |             | 50,196 |   | 136,112 |   |
| Other amortization                                                                                  |       | 67,837                                      |             | 67,837 |   | 66,725 |   |
| Unrealized loss on available-for-sale securities                                                    |       | (3,696                                      | )                | — |   | — |   |
| Changes in operating assets and liabilities                                                         |       |                                        |             |   |   |   |   |
| (Increase) decrease in:                                                                             |       |                                        |             |   |   |   |   |
| Accounts receivable, net                                                                            |       | (728,001                                    | )                | (165,987 | ) | (452,303 | ) |
| Accounts receivable—leasehold incentives                                                       |       | 1,011,201                                   |             | 221,963 |   | (1,333,438 | ) |
| Income tax receivable                                                                               |       | 1,488,931                                   |             | (711,764 | ) | (927,371 | ) |
| Merchandise inventory                                                                               |       | (7,723,540                                  | )                | (4,256,193 | ) | (3,811,490 | ) |
| Prepaid expenses and other assets                                                                   |       | (169,771                                    | )                | 75,979 |   | (189,020 | ) |
| Increase (decrease) in:                                                                             |       |                                        |             |   |   |   |   |
| Accounts payable                                                                                    |       | 6,860,498                                   |             | 2,107,957 |   | (562,718 | ) |
| Accrued expenses                                                                                    |       | 2,560,927                                   |             | 849,259 |   | 765,350 |   |
| Deferred rent and lease incentives                                                                  |       | 1,241,343                                   |             | 2,288,519 |   | 2,245,616 |   |
| Net cash provided by operating activities                                                           |       | 25,202,345                                  |             | 16,741,521 |   | 7,648,340 |   |
| Investing activities:                                                                               |       |                                        |             |   |   |   |   |
| Acquisition of property and equipment                                                               |       | (25,258,595                                 | )                | (20,446,122 | ) | (11,442,985 | ) |
| Acquisition of intangibles                                                                          |       | —                                      |             | — |   | (90,000 | ) |
| Proceeds from sale of property and equipment                                                        |       | 608,022                                     |             | 35,600 |   | — |   |
| Purchase of available-for-sale securities                                                           |       | (1,751,174                                  | )                | — |   | — |   |
| Payments received on notes receivable, related   party                                              |       | 270,301                                     |             | — |   | — |   |
| Payments received for premiums paid on   split-dollar life insurance                                |       | 659,852                                     |             | — |   | — |   |
| Notes receivable, related party—insurance premiums                                             |       | (4,729                                      | )                | (36,163 | ) | (35,279 | ) |
| Increase in split-dollar life insurance premiums                                                    |       | (81,991                                     | )                | (65,364 | ) | (30,238 | ) |
| Net cash used in investing activities                                                               |       | (25,558,314                                 | )                | (20,512,049 | ) | (11,598,502 | ) |
| Financing activities:                                                                               |       |                                        |             |   |   |   |   |
| Borrowings under credit facility                                                                    |       | —                                      |             | 5,847,041 |   | 5,189,283 |   |
| Repayments under credit facility                                                                    |       | (27,236,324                                 | )                | (500,000 | ) | (1,000,000 | ) |
| Repayments under notes payable                                                                      |       | —                                      |             | (119,412 | ) | (345,407 | ) |
| Repayments under notes payable, related party                                                       |       | (923,606                                    | )                | (533,150 | ) | (505,537 | ) |
| Capital lease finance obligation payments                                                           |       | (485                                        | )                | — |   | — |   |
| Distributions to noncontrolling interests                                                           |       | (810,000                                    | )                | (990,000 | ) | (1,080,000 | ) |
| Purchase of remaining 45% noncontrolling interest   in BVC                                          |       | (10,050,880                                 | )                | — |   | — |   |
| Proceeds from common stock issued in initial   public offering, net of commissions                  |       | 58,134,770                                  |             | — |   | — |   |
| Excess tax benefit from stock-based compensation                                                    |       | 620,138                                     |             | — |   | — |   |
| Equity issuance costs and BVC transaction costs                                                     |       | (2,460,196                                  | )                | — |   | — |   |
| Loan fees paid                                                                                      |       | (4,049                                      | )                | (1,972 | ) | (2,500 | ) |
| Net cash provided by financing activities                                                           |       | 17,269,368                                  |             | 3,702,507 |   | 2,255,839 |   |
| Net increase (decrease) in cash and cash   equivalents                                              |       | 16,913,399                                  |             | (68,021 | ) | (1,694,323 | ) |
| Cash and cash equivalents, beginning of year                                                        |       | 377,549                                     |             | 445,570 |   | 2,139,893 |   |
| Cash and cash equivalents, end of year                                                              |       | $                                           |  17,290,948 |   | 377,549 |   | 445,570 |   |
| Supplemental disclosures of cash flow information:                                                  |       |                                        |             |   |   |   |   |
| Cash paid for interest, net of capitalized   interest of $25,000, $32,000 and $21,000, respectively |       | $                                           |  524,391    |   | 615,425 |   | 802,901 |   |
| Cash paid for interest on capital lease finance   obligations                                       |       | 39,197                                      |             | — |   | — |   |
| Income taxes paid                                                                                   |       | 519,231                                     |             | 11,589 |   | 2,918,326 |   |
| Supplemental disclosures of non-cash investing and   financing activities:                          |       |                                        |             |   |   |   |   |
| Acquisition of property and equipment not yet paid                                                  |       | $                                           |  5,007,169  |   | 2,055,213 |   | 1,103,969 |   |
| Property acquired through capital lease financing   obligations                                     |       | 5,526,327                                   |             | — |   | — |   |
| Equity issuance costs not yet paid                                                                  |       | 256,420                                     |             | — |   | — |   |
| Tax benefit associated with acquisition of   noncontrolling interest in BVC                         |       | 3,591,931                                   |             | — |   | — |   |

 

See accompanying notes to consolidated financial statements.

 

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**NATURAL GROCERS BY VITAMIN COTTAGE, INC.**

**Consolidated Statements of Changes in Stockholders’ Equity and Comprehensive Income**

**Fiscal years ended September 30, 2012, 2011 and 2010**

 
|                                                                                                                                    |       |                                                                                                    |       |                                                           |       |                    |       |              |       |             |       |                                    |       |                   |       |               |       |                   |       |                  |       |         |       |        |       |   |       |   |   |      |   |   |       |   |
|-----------------------------------------------------------------------------------------------------------------------------------------|------------|---------------------------------------------------------------------------------------------------------|------------|----------------------------------------------------------------|------------|-------------------------|------------|-------------------|------------|------------------|------------|-----------------------------------------|------------|------------------------|------------|--------------------|------------|------------------------|------------|-----------------------|------------|--------------|------------|-------------|------------|--------|------------|--------|--------|-----------|--------|--------|------------|--------|
| ** **                                                                                                                              | ** ** | **Common Stock – Vitamin Cottage Natural   Food Markets, Inc.** | ** ** | **Common Stock –   NGVC, $0.001 par** | ** ** | **Accumulated   other** | ** ** | **Additional**    | ** ** | ** **       | ** ** | **Natural   Grocers by   Vitamin** | ** ** | ** **             | ** ** | **Total**          | ** ** |
| ** **                                                                                                                              | ** ** | **Class A**                                                                                        | ** ** | **Class B**                                               | ** ** | **value**               | ** ** | **comprehensive** | ** ** | **paid in** | ** ** | **Retained**                            | ** ** | **Cottage, Inc.** | ** ** | **Noncontrolling** | ** ** | **stockholders’** | ** ** |
| ** **                                                                                                                              | ** ** | **Shares**                                                                                              | ** ** | **Amount**                                                     | ** ** | **Shares**              | ** ** | **Amount**        | ** ** | **Shares**       | ** ** | **Amount**                              | ** ** | **loss**               | ** ** | **capital**        | ** ** | **earnings**           | ** ** | **Total equity** | ** ** | **Interest** | ** ** | **equity**  | ** ** |
| Balances   September 30, 2009                                                                                                      |       | 1,000                                                                                                   |       | $                                                              | 1,679      |                    | 625,112    |              | $          | 792,676          |       | —                                  |       | $                      | —     |               | $          | —                 |       | $                     | —     |         | $          | 5,694,002   |       | $      | 6,488,357  |   | $      | 1,302,168 |   | $      | 7,790,525  |   |
| Distributions   to noncontrolling interest                                                                                              |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | —             |       | —                 |       | —                |       | (1,080,000   | )          | (1,080,000  | )          |
| Net   income attributable to Natural Grocers by Vitamin Cottage, Inc.                                                              |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | —             |       | 4,407,963              |       | 4,407,963             |       | —       |       | 4,407,963   |       |
| Net   income attributable to noncontrolling interest                                                                                    |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | —             |       | —                 |       | —                |       | 1,188,605    |       | 1,188,605   |       |
| Balances   September 30, 2010                                                                                                      |       | 1,000                                                                                                   |       | 1,679                                                          |       | 625,112                 |       | 792,676           |       | —           |       | —                                  |       | —                 |       | —             |       | 10,101,965             |       | 10,896,320            |       | 1,410,773    |       | 12,307,093  |       |
| Distributions   to noncontrolling interest                                                                                              |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | —             |       | —                 |       | —                |       | (990,000     | )          | (990,000    | )          |
| Net   income attributable to Natural Grocers by Vitamin Cottage, Inc.                                                              |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | —             |       | 3,503,811              |       | 3,503,811             |       | —       |       | 3,503,811   |       |
| Net   income attributable to noncontrolling interest                                                                                    |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | —             |       | —                 |       | —                |       | 1,106,075    |       | 1,106,075   |       |
| Balances   September 30, 2011                                                                                                      |       | 1,000                                                                                                   |       | 1,679                                                          |       | 625,112                 |       | 792,676           |       | —           |       | —                                  |       | —                 |       | —             |       | 13,605,776             |       | 14,400,131            |       | 1,526,848    |       | 15,926,979  |       |
| Distributions   to noncontrolling interest                                                                                              |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | —             |       | —                 |       | —                |       | (810,000     | )          | (810,000    | )          |
| Net   income attributable to noncontrolling interest                                                                                    |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | —             |       | —                 |       | —                |       | 827,772      |       | 827,772     |       |
| Accumulated   other comprehensive loss                                                                                                  |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | (3,696                 | )          | —             |       | —                 |       | (3,696                | )          | —       |       | (3,696      | )          |
| Net   income attributable to Natural Grocers by Vitamin Cottage, Inc.                                                              |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | —             |       | 6,648,800              |       | 6,648,800             |       | —       |       | 6,648,800   |       |
| Exchange   of Vitamin Cottage Natural Food Markets, Inc. stock for common stock of   Natural Grocers by Vitamin Cottage, Inc. |       | (1,000                                                                                                  | )          | (1,679                                                         | )          | (625,112                | )          | (792,676          | )          | 17,378,625       |       | 17,379                                  |       | —                 |       | 776,976            |       | —                 |       | —                |       | —       |       | —      |       |
| Purchase   of noncontrolling interest                                                                                                   |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | 670,056          |       | 670                                     |       | —                 |       | (8,506,930         | )          | —                 |       | (8,506,260            | )          | (1,544,620   | )          | (10,050,880 | )          |
| Tax   benefit of purchase of noncontrolling interest (Note 1)                                                                           |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | 3,591,931          |       | —                 |       | 3,591,931             |       | —       |       | 3,591,931   |       |
| Shares   issued upon consummation of initial public offering, net of $4,375,735   underwriter discounts and commissions (Note 1)        |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | 4,167,367        |       | 4,167                                   |       | —                 |       | 58,130,603         |       | —                 |       | 58,134,770            |       | —       |       | 58,134,770  |       |
| Issuance   costs                                                                                                                        |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | (2,716,616         | )          | —                 |       | (2,716,616            | )          | —       |       | (2,716,616  | )          |
| Stock-based   compensation                                                                                                              |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | 156,136          |       | 156                                     |       | —                 |       | 779,823            |       | —                 |       | 779,979               |       | —       |       | 779,979     |       |
| Tax   benefit of stock-based compensation                                                                                               |       | —                                                                                                  |       | —                                                         |       | —                  |       | —            |       | —           |       | —                                  |       | —                 |       | 620,138            |       | —                 |       | 620,138               |       | —       |       | 620,138     |       |
| Balances   September 30, 2012                                                                                                      |       | —                                                                                                  |       | $                                                              | —     |                    | —     |              | $          | —           |       | 22,372,184                              |       | $                      | 22,372     |               | $          | (3,696                 | )          | $                     | 52,675,925 |         | $          | 20,254,576  |       | $      | 72,949,177 |   | $      | —    |   | $      | 72,949,177 |   |

 

See accompanying notes to consolidated financial statements.

 

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**Natural Grocers by Vitamin Cottage, Inc.**

** **

**Notes to Consolidated Financial Statements**

** **

**September 30, 2012 and 2011**

 

**1. Organization**

 

*Nature of Business*

 

Natural Grocers by Vitamin Cottage, Inc. (Natural Grocers or the holding company) and its consolidated subsidiaries (collectively, the Company) operate retail stores that specialize in natural and organic groceries and dietary supplements. The Company operates its retail stores under its trademark *Natural Grocers by Vitamin Cottage*® with 59 stores as of September 30, 2012, including 31 stores in Colorado, ten in Texas, four in New Mexico, three in Kansas, two in Wyoming, three in Arizona, and one in each of the following states; Utah, Oklahoma, Missouri, Montana, Idaho and Nebraska, as well as a bulk food repackaging facility and distribution center in Colorado. The Company had 49 and 39 stores as of September 30, 2011 and 2010, respectively.

 

**2. Basis of Presentation and Summary of Significant Accounting Policies**

 

*Principles of Consolidation*

 

The holding company was incorporated in Delaware on April 9, 2012. The accompanying consolidated financial statements include all the accounts of the Company’s wholly owned subsidiaries, Vitamin Cottage Natural Food Markets, Inc. (the operating company), Vitamin Cottage Two Ltd. Liability Company (VC2), Natural Systems, LLC and Boulder Vitamin Cottage Group, LLC (BVC). The operating company formed the holding company in order to facilitate the purchase of the remaining noncontrolling interest in BVC and consummation of the initial public offering (IPO).  Prior to the Company’s IPO on July 25, 2012, the Company had a majority 55% ownership of BVC.  Prior to the settlement of the IPO, the Company issued 670,056 shares of stock in the holding company and paid $10,050,880 in cash to purchase the remaining 45% noncontrolling interest in BVC.  Effective October 31, 2012, BVC merged with and into the operating company and ceased to exist.  Prior to the merger, BVC owned five *Natural Grocers by Vitamin Cottage* retail stores, which were managed by the operating company.  All significant intercompany balances and transactions have been eliminated in consolidation.

 

*Initial Public Offering*

 

The holding company was incorporated in anticipation of the Company’s IPO.  Prior to the IPO, the holding company was a wholly owned subsidiary of the operating company.  In connection with the Company’s IPO, the Company completed a reorganization in which a) the existing shareholders of the operating company exchanged capital stock of the operating company for shares of common stock of the holding company and b) the operating company purchased the remaining 45% noncontrolling interest in BVC for a combination of cash and common stock of the holding company as described above.  The holding company’s only material asset is its direct 100% ownership in the operating company.  On July 25, 2012, the Company issued 4,167,367 shares to the public.  Simultaneously with the IPO, certain selling shareholders sold 4,046,918 shares to the public resulting in no additional proceeds to the Company.

 

The following table summarizes the shares issued in the IPO.

 
| Shares sold by the Company                                   |   | 4,167,367 |   |
|--------------------------------------------------------------|--------|-----------|--------|
| Shares sold by the original operating company   shareholders |   | 4,046,918 |   |
| Total shares issued in IPO                                   |   | 8,214,285 |   |

 

The following table details total shares outstanding as of September 30, 2012.

 
| Shares held by institutional and individual owners                         |   | 8,214,285  |   |
|----------------------------------------------------------------------------|--------|------------|--------|
| Shares issued in connection with purchase of BVC   noncontrolling interest |   | 670,056    |   |
| Shares issued in connection with restricted stock   award                  |   | 156,136    |   |
| Shares held by the original operating company   shareholders               |   | 13,331,707 |   |
| Total shares outstanding as of September 30,   2012                   |   | 22,372,184 |   |

 

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Based on the public offering price of $15.00, the Company received gross proceeds from the issuance of 4,167,367 shares issued to the public in the IPO of $62,510,505, and paid underwriting costs of 7%, or $4,375,735, for net proceeds of $58,134,770.  The Company recorded the proceeds received from the IPO as cash and cash equivalents and recorded the issuance of common stock at par value, with the remaining amount being recorded as additional paid in capital.  The Company also incurred issuance costs of approximately $2.7 million.

 

The Company accounted for the acquisition of the BVC noncontrolling interest, as described above, as an equity transaction.  Since the transaction is treated as an equity transaction, the transaction costs are also reflected as a reduction of equity and a financing activity in the statement of cash flows.  The Company recorded the issuance of the 670,056 shares in common stock at par value, reduced cash and cash equivalents by approximately $10.1 million, eliminated approximately $1.5 million in noncontrolling interest on the balance sheet in July 2012, and recorded the remaining amount as additional paid in capital.  As a result of the acquisition of the remaining noncontrolling interest, the Company is entitled to tax deductions to the extent of any step up in tax basis on the assets of BVC, limited to the cash consideration paid.  Accordingly, the tax basis in excess of book basis at the date of purchase resulted in deferred tax assets of approximately $3.6 million.

 

As of September 30, 2012, the Company has used the proceeds from the IPO to pay down all outstanding amounts under the credit facility, pay the cash portion of the BVC purchase, pay expenses associated with the IPO and pay the cash portion of restricted stock awards.  The following table illustrates the use of proceeds received from the IPO as of September 30, 2012:

 
| ** **                                                                       | ** ** | **As of September 30, 2012** | ** ** |
|----------------------------------------------------------------------------------|------------|--------------------------------------------------|------------|
| Repayment of term loan and amounts outstanding   under revolving credit facility |       | $                                                | 26,397,060 |   |
| Cash portion of the purchase price paid to acquire   BVC noncontrolling interest |       | 10,050,880                                       |       |
| Expenses associated with IPO (excluding amounts   accrued)                       |       | 2,460,196                                        |       |
| Cash portion of restricted stock award                                           |       | 334,579                                          |       |
| Total use of proceeds received from IPO                                          |       | $                                                | 39,242,715 |   |

 

*Use of Estimates*

 

The preparation of financial statements in conformity with generally accepted accounting principles in the United States of America (GAAP) requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. Management reviews its estimates on an ongoing basis, including those related to allowances for self-insurance reserves, valuation of inventories, useful lives for depreciation and amortization of property and equipment, valuation allowances for deferred tax assets and liabilities and litigation based on currently available information. Changes in facts and circumstances may result in revised estimates and actual results could differ from those estimates.

 

*Segment Information*

 

The Company has one reporting segment, natural and organic retail stores. Financial Accounting Standards Board (FASB) Accounting Standards Codification (ASC) Topic 280, *Segment Reporting*, establishes standards for reporting information about a company’s operating segments.

 

*Cash and Cash Equivalents*

 

Cash and cash equivalents include currency on hand, demand deposits with banks, money market funds and credit and debit card transactions which typically settle within three business days of year end. The Company considers all highly liquid investments with an original maturity of 90 days or less to be cash equivalents.

 

*Accounts Receivable*

 

Accounts receivable consists primarily of receivables from vendors for certain promotional programs, primarily newsletter advertising, and other miscellaneous receivables and are presented net of any allowances for doubtful accounts. The Company had no allowances for doubtful accounts as of September 30, 2012 and 2011. Accounts receivable—leasehold incentives consist of receivables due from landlords for tenant allowances.

 

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* *

*Concentration of Credit Risk*

 

Financial instruments that potentially subject the Company to a concentration of credit risk consist primarily of investments in cash and cash equivalents, accounts receivable and investments in available-for-sale securities. The Company’s cash and cash equivalent account balances did not exceed the Federal Deposit Insurance Corporation’s federally insured limits as of September 30, 2012. The Company records accounts receivable from the sale of newsletter advertising to vendors. If the accounts are not paid timely, the Company has the right to set off the amount of unpaid receivable balance with the amount owed to the other party for vendor product invoices. The Company evaluates the ability to collect the receivables and believes the amounts appearing on the consolidated balance sheets to be fully collectible as of September 30, 2012 and 2011. Accordingly, no allowance for doubtful accounts has been recorded for the years ended September 30, 2012, 2011 and 2010.

 

*Vendor Concentration*

 

For the years ended September 30, 2012, 2011 and 2010, purchases from the Company’s largest vendor and one of its subsidiaries represented approximately 53%, 53% and 52% of all product purchases made during the respective periods. However, the Company believes that, if necessary, alternate vendors could supply similar products in adequate quantities to avoid disruption to operations.

 

*Merchandise Inventory*

 

Merchandise inventory consists of goods held for sale. The cost of inventory includes certain costs associated with the preparation of inventory for sale including inventory overhead costs. Merchandise inventory is carried at the lower of cost or market. Cost is determined using the weighted average cost method.

 

*Property and Equipment*

 

Property and equipment is stated at historical cost less accumulated depreciation. In accordance with FASB ASC Topic 835, *Interest*, the Company capitalizes interest, if applicable, as part of the historical costs of leasehold improvements. Depreciation is provided using the straight-line method over the following estimated useful lives of the related assets.

 
| ** **                     | ** ** | **Useful lives (in   years)** | ** ** |
|--------------------------------|------------|-----------------------------------------|------------|
| Land improvements              |       | 6 - 15                                  |       |
| Leasehold improvements         |       | 2 - 20                                  |       |
| Capitalized real estate leases |       | 40                                      |       |
| Fixtures and equipment         |       | 5 - 7                                   |       |
| Computer hardware and software |       | 3 - 5                                   |       |

 

For leasehold and land improvements, depreciation is recorded over the shorter of the useful lives or the lease terms. The estimated useful lives range from two to 20 years. Maintenance, repairs and renewals that neither add to the value of the property nor appreciably prolong its life are charged to expense as incurred. Gains and losses on disposition of property and equipment are included in store expenses in the year of disposition, and primarily relate to store relocations.

 

The Company capitalizes certain costs incurred with developing or obtaining internal-use software. Capitalized software costs are included in property and equipment in the consolidated balance sheets and are amortized over the estimated useful lives of the software. Software costs that do not meet capitalization criteria are expensed as incurred.

 

*Fair Value of Financial Instruments*

 

The Company records its financial assets and liabilities at fair value in accordance with the framework for measuring fair value in authoritative guidance. The framework establishes a fair value hierarchy that distinguishes between assumptions based on market data (observable inputs) and the Company’s own assumptions (unobservable inputs). The three levels of the fair value hierarchy are as follows:

 
| Level 1— | Quoted   market prices in active markets for identical assets or liabilities;                                                                                                                                                                                                                                                  |
|--------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Level 2— | Inputs   other than Level 1 inputs such as quoted prices for similar assets or   liabilities or model-driven valuations in which all significant inputs are   observable or can be derived principally from or corroborated by observable   market data for substantially the full term of the assets or liabilities; and |
| Level 3— | Unobservable   inputs to the valuation methodology that are significant to the measurement   of fair value assets                                                                                                                                                                                                              |

 

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|   | and   liabilities. |
|--------|--------------------|

 

*Goodwill and Intangible Assets*

 

In September 2011, the FASB issued Accounting Standards Update (ASU) No. 2011-08, *Intangibles—Goodwill and Other (Topic 350); Testing Goodwill for Impairment*. The objective of the update is to simplify how entities test goodwill for impairment. The update allows for a company to first evaluate qualitative factors, including relevant events and circumstances, to determine whether it is more likely than not that the fair value of a reporting unit is less than its carrying amount. The Company early adopted the provisions of this update as of September 30, 2011. Goodwill is reviewed for impairment at least annually. In order to test goodwill for impairment, the Company first evaluates qualitative factors, including relevant events and circumstances, to determine whether it is more likely than not that the fair value of a reporting unit is less than its carrying amount. If it is not more likely than not that the fair value of a reporting unit is less than its carrying amount, the two-step impairment test is not necessary. If it is determined that it is more likely than not that the fair value of a reporting unit is less than its carrying amount, then the Company would perform the two-step impairment test. Under the first step, the fair value of the reporting unit is compared with its carrying value (including goodwill). If the fair value of the reporting unit is less than its carrying value, an indication of goodwill impairment exists for the reporting unit and the Company must perform step two of the impairment test (measurement). Under step two, an impairment loss is recognized for any excess of the carrying amount of the reporting unit’s goodwill over the implied fair value of that goodwill.

 

*Impairment of Intangible and Long-Lived Assets*

 

Intangible assets primarily consist of goodwill, trademarks, favorable operating leases and covenants-not-to-compete. Goodwill and the Vitamin Cottage trademark have indefinite lives and are not amortized; rather, they are tested for impairment at least annually. The Company’s annual impairment testing is performed as of September 30. Intangible assets with definite lives are amortized over their estimated useful lives. The Company evaluates the reasonableness of the useful lives of these intangibles at least annually.

 

Long-lived assets, such as property and equipment and purchased intangible assets subject to amortization, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable. The Company aggregates long-lived assets at the store level which the Company considers to be the lowest level in the organization for which independent identifiable cash flows are available. If circumstances require a long-lived asset or asset group to be tested for possible impairment, the Company first compares undiscounted cash flows expected to be generated by that store to its carrying value. If the carrying value of the long-lived asset or asset group is not recoverable on an undiscounted cash flow basis, impairment is recognized to the extent that the carrying value exceeds its fair value. The Company considers factors such as historic and forecasted operating results, trends and future prospects, current market value, significant industry trends and other economic and regulatory factors in performing these analyses.

 

*Deferred Financing Costs*

 

Certain costs incurred with borrowings or establishment of credit facilities are deferred. These costs are amortized over the life of the borrowing or the life of the credit facility using the effective interest method.

 

*Self-Insurance*

 

The Company is self-insured for certain losses relating to employee medical and dental benefits. Stop-loss coverage has been purchased to limit exposure to any significant level of claims. Self-insured losses are accrued based upon the Company’s estimates of the aggregate claims incurred but not reported using historical experience. The estimated accruals for these liabilities could be significantly affected if future occurrences and claims differ from historical trends.

 

*Revenue Recognition*

 

Revenue is recognized at the point of sale, net of in-house coupons, discounts, returns and allowances. Sales taxes are not included in sales. The Company charges sales tax on all taxable customer purchases and remits these taxes monthly to the appropriate taxing jurisdiction. The Company also ships certain products ordered through its Internet site. Revenue is recognized on Internet sales at the time the products are shipped to the customers. The Company records a deferred revenue liability within accrued expenses when it sells Natural Grocers gift cards or issues gift cards to employees, and records a sale when a customer redeems the gift card. The gift cards do not expire. The Company currently does not record breakage for unused portions of gift cards.

 

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*Cost of Goods Sold and Occupancy Costs*

 

Cost of goods sold and occupancy costs includes the cost of inventory sold during the period net of discounts and allowances, as well as, distribution, shipping and handling costs, store occupancy costs and costs of the bulk food repackaging facility and distribution center. The amount shown is net of various rebates from third-party vendors in the form of quantity discounts and payments. Vendor consideration associated with product discounts is recorded as either a reduction of merchandise inventory or cost of goods sold.

 

*Store Expenses*

 

Store expenses consist of store-level expenses such as salaries and benefits, supplies, utilities, depreciation, gain or loss on disposal of assets and other related costs associated with operations support. Store expenses also include purchasing support services and advertising and marketing costs.

 

*Administrative Expenses*

 

Administrative expenses consist of salaries and benefits, occupancy costs, depreciation, office supplies, hardware and software expenses, professional services expenses and other general and administrative expenses.

 

*Pre-Opening and Relocation Expenses*

 

Costs associated with the opening of new stores or relocating existing stores are expensed as incurred.

 

*Leases*

 

The Company leases retail stores, a bulk food repackaging facility and distribution center and administrative offices under long-term operating leases. These leases include scheduled increases in minimum rents and renewal provisions at the option of the Company. The lease term for accounting purposes commences with the date the Company takes possession of the space and ends on the later of the primary lease term or the expiration of any renewal periods that are deemed to be reasonably assured at the inception of the lease. The Company accounts for operating leases with rent holidays and escalating payment terms by recognizing the associated expense on a straight-line basis over the lease term. For certain leases, the Company has also received cash from landlords to compensate for costs incurred by the Company in making the store locations ready for operation (leasehold incentives or tenant allowances). Leasehold incentives received from a landlord are deferred and recognized on a straight-line basis as a reduction to rent expense over the lease term.

 

The Company recently entered into lease agreements with a developer for certain build to suit store locations.  Under the terms of the lease agreements, the Company is responsible for contributing certain amounts towards the cost of construction.  As a result of this involvement, the Company was deemed the “owner” for accounting purposes during the construction period, and is required to capitalize the construction costs on its balance sheet.  Upon completion of the project, the Company performs a sale-leaseback analysis pursuant to ASC Topic 840, *Leases,*to determine if the Company can remove the assets from its balance sheet.  In accordance with the terms of the lease agreements, the Company is not reimbursed for the amounts contributed towards the cost of construction and is therefore deemed to have “continuing involvement” per ASC Topic 840, *Leases*, which prevents the Company from derecognizing the assets on the balance sheet when construction is complete and requires the Company to account for the leases as assets and related capital lease finance obligations.  As provided by ASC Topic 840, *Leases,*the Company records the fair market value of the building as an asset on its balance sheet, and records a capital lease finance obligation equal to the fair market value of the building less the amount the Company contributed towards construction.  The Company does not record rent expense for the capital leases, but rather rental payments under the capital leases are recognized as a reduction of the capital lease finance obligation and as interest expense.  The capital lease asset is depreciated on a straight line basis over a 40 year life for buildings and an indefinite life for land. The Company had four stores as of September 30, 2012 that were build to suit store locations where the Company was deemed to be the owner during the construction period.  Two of the stores opened in the fourth quarter of fiscal year 2012 and are reflected as capitalized real estate leases and capital lease finance obligations at September 30, 2012.

 

Two of the stores were under construction as of September 30, 2012 and are scheduled to open in the first quarter of fiscal year 2013.  Construction costs for the two stores currently under construction are reflected in construction in process and capital lease finance obligations.

 

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*Advertising and Marketing*

 

Advertising and marketing costs are expensed as incurred and are included in store expenses and pre-opening and relocation expenses in the consolidated statements of income. Total advertising and marketing expenses for the years ended September 30, 2012, 2011 and 2010 were approximately $5.1 million, $5.4 million and $3.9 million, respectively, net of vendor reimbursements received for newsletter advertising. Advertising expense reimbursements received from vendors totaled approximately $1.3 million, $1.1 million and $651,000 for the years ended September 30, 2012, 2011 and 2010, respectively.

 

*Investments*

 

Available-for-sale investments are recorded at fair value.  Unrealized holding gains and losses on available-for-sale investments are excluded from earnings and are reported as a separate component of stockholders’ equity until realized.  A decline in the fair value of any available-for-sale security below cost that is deemed to be other-than-temporary for a period greater than two fiscal quarters results in a reduction of the fair value.  Declines in fair value deemed to be other-than-temporary are charged against net earnings.  Investments that have an original maturity date of less than one year are classified as short-term assets and investments that have an original maturity date greater than one year are classified as long-term assets.

 

*Comprehensive Income*

 

Comprehensive income consists of net income and unrealized gains and losses on available-for-sale securities.  Comprehensive income is reflected in the consolidated statements of changes in stockholders’ equity and comprehensive income.

 

*Stock-Based Compensation*

 

The Company adopted an Omnibus Incentive Plan in connection with the IPO on July 25, 2012.  As of September 30, 2012, the Company had issued restricted stock units to its Chief Financial Officer and a member of the Board of Directors.  Restricted common stock is granted at the market price of the stock on the day of grant and is expensed over the applicable vesting period.

 

The benefits of tax deductions in excess of recognized compensation costs are reported as a credit to additional-paid-in capital and as operating cash flows, but only when such excess tax benefits are realized by a reduction to current taxes payable.

 

*Income Taxes*

 

The Company accounts for income taxes using the asset and liability method. This method requires recognition of deferred tax assets and liabilities for expected future tax consequences of temporary differences that currently exist between the tax basis and financial reporting basis of the Company’s assets and liabilities. Deferred tax assets and liabilities are measured using enacted tax rates in the respective jurisdictions in which the Company operates.

 

The Company considers the need to establish valuation allowances to reduce deferred income tax assets to the amounts the Company believes are more likely than not to be recovered.

 

The Company recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than 50% likely of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. Although the Company believes that its estimates are reasonable, actual results could differ from these estimates. In addition, the Company is subject to periodic audits and examinations by the Internal Revenue Service and other state and local taxing authorities.

 

Any interest or penalties incurred related to income taxes are expensed as incurred and treated as permanent differences for tax purposes.

 

*Noncontrolling Interest in Consolidated Financial Statements*

 

Prior to the Company’s IPO on July 25, 2012, the Company had a majority 55% ownership of BVC which owned five *Natural Grocers by Vitamin Cottage* retail stores managed by the operating company.  Subsequent to the IPO the Company purchased the remaining 45% noncontrolling interest in BVC.  Noncontrolling interest in the Company’s consolidated financial statements relates to the noncontrolling 45% ownership in BVC prior to the purchase. Net income attributable to noncontrolling interest and net income attributable to the Company are reported separately in the consolidated statements of income. Additionally, noncontrolling interest in the consolidated subsidiaries of the Company is reported as a separate component of equity in the consolidated balance sheet, apart from the Company’s equity.

 

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*Reclassifications*

 

Where appropriate, we have reclassified prior years’ financial statements to conform to current year presentation.

 

*Recent Accounting Pronouncements*

 

In July 2012, the FASB issued ASU No. 2012-02, *Testing Indefinite-Lived Intangible Assets for Impairment,*which amends ASC 350, *Intangibles — Goodwill and Other. *The amended guidance simplifies how entities test for impairment of indefinite-lived intangible assets.  The amendments permit an entity to first assess qualitative factors to determine whether it is more likely than not that the fair value of the asset is less than its carrying amount as a basis for determining if performing a quantitative test is necessary.  The amendments do not change the impairment losses.  The amendments are effective for annual and interim impairment tests performed for fiscal years beginning after September 15, 2012.  The provisions are effective for the Company’s first quarter of fiscal year 2013.  The Company does not expect the adoption of these provisions to have a significant effect on the Company’s consolidated financial statements.

 

In June 2011, the FASB issued ASU No. 2011-05, *Presentations of Comprehensive Income*, which amends ASC 220, *Comprehensive Income*. The update eliminates the option of presenting the components of other comprehensive income as part of the statement of stockholders’ equity. Instead, comprehensive income must be reported either in a single continuous statement of comprehensive income, which contains two sections, net income and other comprehensive income, or in two separate but consecutive statements. In December 2011, the FASB issued ASU No. 2011-12, *Deferral of the Effective Date for Amendments to the Presentation of Reclassifications of Items Out of Accumulated Other Comprehensive Income in Accounting Standards Update No. 2011-05*, which defers the implementation requirement in ASU No. 2011-05 to present on the face of the financial statements the effects of reclassifications out of accumulated other comprehensive income on the components of net income and other comprehensive income. The amended guidance specifies that entities should continue to report reclassifications out of accumulated other comprehensive income consistent with presentation requirements in effect before ASU No. 2011-05. The guidance provided in ASU No. 2011-05 and ASU No. 2011-12 is effective for fiscal years and interim periods within those years, beginning after December 15, 2011. The provisions are effective for the Company’s first quarter of fiscal year 2013. The Company does not expect the adoption of these provisions to have a significant effect on the Company’s consolidated financial statements.

 

*Immaterial Adjustments to Previously Reported Consolidated Statements of Cash Flows*

 

The Company has recorded immaterial adjustments of approximately $1,104,000 and $340,000 to increase previously reported net cash provided by operating activities and to increase previously reported net cash used in investing activities to properly reflect cash paid for the acquisition of property and equipment for the years ended September 30, 2011 and 2010, respectively. These adjustments had no impact on the net change in cash and cash equivalents for the respective periods.

 

**3. Earnings Per Share**

 

Basic earnings per share (EPS) excludes dilution and is computed by dividing net income attributable to Natural Grocers by Vitamin Cottage, Inc. stockholders by the weighted average shares outstanding during the period. Diluted EPS reflects the potential dilution that could occur if securities or other contracts to issue common stock were exercised, resulting in the issuance of common stock that would then share in the earnings of the Company. Presented below is basic and diluted EPS for the years ended September 30, 2012, 2011 and 2010:

 
| ** **                                                                           | ** ** | **Year ended September 30,** | ** ** |
|--------------------------------------------------------------------------------------|------------|---------------------------------------------|------------|
| ** **                                                                           | ** ** | **2012**                                    | ** ** | **2011** | ** ** | **2010** | ** ** |
| Net income attributable to Natural Grocers by   Vitamin Cottage, Inc.           |       | $                                           | 6,648,800  |   | 3,503,811 |   | 4,407,963 |   |
|                                                                                 |       |                                        |       |   |   |   |   |
| Weighted average common shares outstanding                                           |       | 22,372,184                                  |       | 22,372,184 |   | 22,372,184 |   |
| Effect of dilutive securities                                                        |       | 90,909                                      |       | 89,221 |   | 89,221 |   |
| Weighted average common shares outstanding   including effect of dilutive securities |       | 22,463,093                                  |       | 22,461,405 |   | 22,461,405 |   |
|                                                                                 |       |                                        |       |   |   |   |   |
| Basic earnings per share                                                             |       | $                                           | 0.30       |   | 0.16 |   | 0.20 |   |
| Diluted earnings per share                                                           |       | $                                           | 0.30       |   | 0.16 |   | 0.20 |   |

 

The Company did not declare any dividends in the years ended September 30, 2012, 2011 and 2010.

 

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As of September 30, 2012, the Company had 50,000,000 shares of common stock authorized and 22,372,184 shares outstanding as well as 10,000,000 shares of preferred common stock authorized with none outstanding.

 

**4.  Investments**

 

The Company had money market fund investments that are classified as cash and cash equivalents of approximately $246,000 as of September 30, 2012.  The Company also had available-for-sale securities, generally consisting of certificates of deposit, corporate bonds and municipal bonds, totaling approximately $1.8 million, of which approximately $777,000 were classified as short-term. At September 30, 2012, the average effective maturities of the Company’s short-term and long-term investments were approximately 8 and 17 months, respectively.  During the year ended September 30, 2012, the Company recorded interest income of approximately $2,400 and recorded expense relating to amortized premiums paid of approximately $1,800.  The Company had no money market fund investments or available-for-sale investments as of September 30, 2011.

 

As of September 30, 2012, available-for-sale securities totaling approximately $1.8 million were in unrealized loss positions with $3,696 recorded in accumulated other comprehensive income for temporary declines in fair value, consisting of three securities in gain positions and nine securities in loss positions due to the amortization of premiums paid to acquire the securities.

 

The Company established an investment policy with the objective to achieve maximum yields on invested funds while protecting principal, as well as ensuring that funds will be available to meet operating cash flow requirements.  The investment policy establishes the type of investments that are acceptable, requires that each investment have a certain high level of rating as established by Standard and Poor’s and/or Moody’s and limits the amount of any one investment that may be held based on the market value of the total funds at the time of investment purchase. As of September 30, 2012, the Company’s investments in available-for-sale securities were in compliance with the Company’s investment policy.

 

**5. Fair Value Measurements**

 

The Company records its financial assets and liabilities at fair value in accordance with the framework for measuring fair value in authoritative guidance. The framework establishes a fair value hierarchy that distinguishes between assumptions based on market data (observable inputs) and the Company’s own assumptions (unobservable inputs).

 

As of September 30, 2012 and 2011, the Company had the following financial assets and liabilities that were subject to fair value measurements according to the fair value hierarchy:

 
| ** **                                        | ** ** | ** **        | ** ** | **As of September 30,** | ** ** |
|---------------------------------------------------|------------|-------------------|------------|----------------------------------------|------------|
| ** **                                        | ** ** | ** **        | ** ** | **2012**                               | ** ** | **2011** | ** ** |
| ** **                                        | ** ** | **Input   Level** | ** ** | **Carrying   Amount**                  | ** ** | **Fair Value** | ** ** | **Carrying   Amount** | ** ** | **Fair Value** | ** ** |
| Cash and cash equivalents:                        |       |              |       |                                   |       |   |   |   |   |   |   |
| Money market fund                                 |       | 1                 |       | $                                      | 245,741    |   | 245,741 |   | — |   | — |   |
| Investments — available-for-sale securities: |       |              |       |                                   |       |   |   |   |   |   |   |
| Certificates of deposit                           |       | 2                 |       | 978,515                                |       | 978,515 |   | — |   | — |   |
| Corporate bonds                                   |       | 2                 |       | 484,715                                |       | 484,715 |   | — |   | — |   |
| Municipal bonds                                   |       | 2                 |       | 287,944                                |       | 287,944 |   | — |   | — |   |
| Liabilities:                                      |       |              |       |                                   |       |   |   |   |   |   |   |
| Long-term debt—term loan                     |       | 2                 |       | —                                 |       | — |   | 16,200,000 |   | 16,200,000 |   |
| Revolving credit facility                         |       | 2                 |       | —                                 |       | — |   | 11,036,324 |   | 11,036,324 |   |
|                                                   |            |                   |            |                                        |            |  |  |  |  |  |  |  |

 

The carrying amounts of the money market fund and available-for-sale securities are carried at fair value. The carrying amounts of the term loan and revolving credit facility approximate fair value for the year ended September 30, 2011.

 

Management believes that the carrying values approximate fair values of notes payable—related party because stated interest rates approximate market rates. The carrying amounts of other financial instruments, including cash and cash equivalents, accounts receivable, accounts payable, accrued liabilities and other accrued expenses approximate fair value because of the short maturity of those instruments.

 

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**6. Property and Equipment**

 

The Company had the following property and equipment balances as of September 30, 2012 and 2011.

 
| ** **                                                               | ** ** | **Useful lives** | ** ** | **As of September 30,** | ** ** |
|--------------------------------------------------------------------------|------------|-----------------------|------------|----------------------------------------|------------|
| ** **                                                               | ** ** | **(in years)**   | ** ** | **2012**                               | ** ** | **2011** | ** ** |
| Land                                                                     |       | n/a                   |       | $                                      | —     |   | 604,855 |   |
| Construction in process                                                  |       | n/a                   |       | 3,642,150                              |       | 1,618,661 |   |
| Capitalized real estate leases, including   unamortized land of $600,000 |       | 40                    |       | 5,204,414                              |       | — |   |
| Land improvements                                                        |       | 6 - 15                |       | 832,239                                |       | 811,304 |   |
| Leasehold improvements                                                   |       | 2 - 20                |       | 45,437,972                             |       | 33,573,855 |   |
| Fixtures and equipment                                                   |       | 5 - 7                 |       | 41,830,033                             |       | 30,666,013 |   |
| Computer hardware and software                                           |       | 3 - 5                 |       | 6,697,106                              |       | 5,362,468 |   |
|                                                                     |       |                  |       | 103,643,914                            |       | 72,637,156 |   |
| Less accumulated depreciation and amortization                           |       |                  |       | (39,041,171                            | )          | (30,899,922 | ) |
| Property and equipment, net                                              |       |                  |       | $                                      | 64,602,743 |   | 41,737,234 |   |

 

Capitalized real estate leases include the assets for two build to suit stores that were open as of September 30, 2012 (see Note 2 and Note 13).

 

Construction in process includes $1.9 million as of September 30, 2012 related to construction costs for build to suit leases in process for which the Company was deemed the owner during the construction period.  These two stores are scheduled to open in the first quarter of fiscal year 2013.

 

Costs capitalized for computer software development for the years ended September 30, 2012 and 2011 were approximately $55,000 and $122,000, respectively, including approximately $42,000 and $110,000, respectively, related to internal staff compensation. Amortization expense related to capitalized computer software development was approximately $487,000 and $530,000 for the years ended September 30, 2012 and 2011, respectively.

 

Total costs capitalized for leasehold improvements and fixtures and equipment include approximately $322,000 and $337,000 related to internal staff compensation, and approximately $19,000 and $32,000 in interest costs for the years ended September 30, 2012 and 2011, respectively.

 

Depreciation and amortization expense for the years ended September 30, 2012, 2011 and 2010 was approximately $9.9 million, $7.6 million and $5.5 million, respectively.

 

**7. Goodwill and Other Intangible Assets**

 

Goodwill and other intangible assets are summarized as follows as of September 30, 2012 and 2011:

 
| ** **                                | ** ** | **Useful lives** | ** ** | **As of September 30,** | ** ** |
|-------------------------------------------|------------|-----------------------|------------|----------------------------------------|------------|
| ** **                                | ** ** | **(in years)**   | ** ** | **2012**                               | ** ** | **2011** | ** ** |
| Amortizable intangible assets:            |       |                  |       |                                   |       |   |   |
| Covenants-not-to-compete                  |       | 5.0                   |       | $                                      | 292,500    |   | 292,500 |   |
| Favorable operating lease                 |       | 5.0                   |       | 339,187                                |       | 339,187 |   |
| Other intangibles                         |       | 0.5                   |       | 22,500                                 |       | 22,500 |   |
| Amortized intangible assets               |       |                  |       | 654,187                                |       | 654,187 |   |
| Less accumulated amortization             |       |                  |       | (626,609                               | )          | (552,772 | ) |
| Amortized intangible assets, net          |       |                  |       | 27,578                                 |       | 101,415 |   |
| Trademark                                 |       | Indefinite            |       | 388,886                                |       | 388,886 |   |
| Total other intangibles, net              |       |                  |       | 416,464                                |       | 490,301 |   |
| Goodwill                                  |       | Indefinite            |       | 511,029                                |       | 511,029 |   |
| Total goodwill and other intangibles, net |       |                  |       | $                                      | 927,493    |   | 1,001,330 |   |

 

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Amortization expense was approximately $74,000, $149,000 and $88,000 for the years ended September 30, 2012, 2011 and 2010, respectively. Amortization expense is expected to be approximately $28,000 in the year ended September 30, 2013. Amortization expense is expected to be zero for the years thereafter.

 

**8. Supplementary Balance Sheet Information**

 

The composition of accrued expenses is summarized as follows as of September 30, 2012 and 2011:

 
| ** **                                            | ** ** | **As of September 30,** | ** ** |
|-------------------------------------------------------|------------|----------------------------------------|------------|
| ** **                                            | ** ** | **2012**                               | ** ** | **2011** | ** ** |
| Payroll and employee-related expenses                 |       | $                                      | 4,412,741  |   | 3,270,900 |   |
| Accrued income, property, sales and use tax   payable |       | 2,197,419                              |       | 1,557,046 |   |
| Deferred revenue related to gift card sales           |       | 555,757                                |       | 495,459 |   |
| Other                                                 |       | 617,513                                |       | 462,094 |   |
| Total accrued expenses                                |       | $                                      | 7,783,430  |   | 5,785,499 |   |

 

**9. Deferred Financing Costs**

 

The Company has capitalized costs incurred in securing its long-term debt (see Note 10). Deferred financing costs, net of accumulated amortization were approximately $55,000 and $89,000 as of September 30, 2012 and 2011, respectively. Accumulated amortization was approximately $832,000 and $794,000 as of September 30, 2012 and 2011, respectively.

 

Total amortization expense for deferred financing costs was approximately $38,000, $50,000 and $136,000 for the years ended September 30, 2012, 2011 and 2010, respectively. Scheduled amortization expenses for the years ending September 30, 2013 and 2014 are approximately $31,000 and $24,000, respectively.

 

**10. Long-Term Debt**

 

*Credit Facility*

 

The Company has a credit facility consisting of a revolving credit facility and a term loan that was fully repaid in fiscal year 2012.  The operating company is the borrower under the credit facility and its obligations under the credit facility are guaranteed by the holding company.

 

The credit facility requires compliance with certain operational and financial covenants (including a leverage ratio, a fixed charge coverage ratio and a revenue ratio). The credit facility also contains certain other limitations on the Company’s ability to incur additional debt, guarantee other obligations, grant liens on assets and make investments or acquisitions as defined in the credit facility agreement. Additionally, the revolving credit facility prohibits the payment of cash dividends to the holding company from the operating company, without the bank’s consent except when no default or event of default exists.

 

If no default or event of default exists dividends are allowed for various audit, accounting, tax, securities, indemnification, reimbursement, insurance and other reasonable expenses in the ordinary course of business.  The Company does not expect such restrictions to impact its ability to meet cash obligations.  The terms and conditions of the agreement for the revolving credit facility and associated documents are customary and include, among other things, guarantees, pledges and subordinations.  At September 30, 2012 and 2011, the Company was in compliance with the debt covenants.

 

*Revolving Credit Facility*

 

On October 31, 2012, the Company amended the agreement governing the revolving credit facility to decrease the credit facility limit from $21.0 million to $15.0 million and to lower the unused commitment fee to 0.20% from 0.375%.  The reduction in the unused commitment fee was retroactive to August 1, 2012. The reduction in the amount available for borrowing is effective October 31, 2012.  As amended during fiscal year 2012, the credit facility matures on June 30, 2014. The Company may borrow, prepay and re-borrow amounts under this revolving credit facility at any time prior to the maturity date.

 

The Company had no amounts outstanding on its revolving credit facility as of September 30, 2012 and approximately $11.0 million outstanding on its revolving credit facility as of September 30, 2011. Proceeds from the Company’s IPO on July 25, 2012 were used to pay off outstanding amounts under the revolving credit facility of $10.6 million.  The commitment fee is 0.20% for any amounts not borrowed under the revolving credit facility as amended in October 2012. Interest is determined by the lender’s administrative agent and is stated at the adjusted LIBOR rate for the interest period plus the lender spread. The lender spread will be reduced by the lender subject to the Company meeting certain financial measures. The average annual interest rates for the years ended September 30, 2012, 2011 and 2010 were 2.54%, 2.38% and 3.88%, respectively.

 

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*Term Loan*

 

The Company had no amounts outstanding as of September 30, 2012 and $16.2 million outstanding as of September 30, 2011. Proceeds from the Company’s IPO on July 25, 2012 were used to prepay the outstanding amounts under the term loan of $15.8 million.  The Company cannot borrow additional amounts on the term loan.  Interest was determined by the lender’s administrative agent and was stated at the alternate base rate for the interest period plus the applicable lender spread. The interest rate at September 30, 2011 was approximately 2.03%. The average interest rate for the years ended September 30, 2012, 2011 and 2010 was approximately 2.02%, 2.19% and 3.46%, respectively.

 

*Notes Payable*

 

The Company entered into a three-year promissory installment note for $1.0 million at 5.50% per annum, which matured January 31, 2011.

 

The revolving credit facility, long-term debt balances and capital lease finance obligations as of September 30, 2012 and 2011 were as follows:

 
| ** **                                                                                | ** ** | **As of September 30,** | ** ** |
|-------------------------------------------------------------------------------------------|------------|----------------------------------------|------------|
| ** **                                                                                | ** ** | **2012**                               | ** ** | **2011** | ** ** |
| Revolving credit facility                                                                 |       | $                                      | —     |   | 11,036,324 |   |
|                                                                                      |       |                                   |       |   |   |
| Long-term debt—term loan                                                             |       | $                                      | —     |   | 16,200,000 |   |
| Capital lease finance obligations, due in monthly   installments through fiscal year 2027 |       | 4,180,584                              |       | — |   |
| Capital lease finance obligations for assets under   construction                         |       | 1,345,258                              |       | — |   |
| Total long-term debt and capital lease finance   obligations                              |       | 5,525,842                              |       | 16,200,000 |   |
| Less current portion                                                                      |       | (11,884                                | )          | (500,000 | ) |
| Long-term debt and capital lease finance   obligations, net of current portion            |       | $                                      | 5,513,958  |   | 15,700,000 |   |

 

The Company has four leases that are included in capital lease finance obligations which include two stores that were open as of September 30, 2012, and two stores that were under construction and are scheduled to open in the first quarter of fiscal year 2013 (see Note 2).  The Company does not record rent expense for these capitalized real estate leases, but rather rental payments under the capital leases are recognized as a reduction of the capital lease finance obligation and as interest expense (see Note 13).

 

**11. Notes Payable—Related Party**

 

The Company has two unsecured notes payable, which bear interest at 5.33% annually and mature in October 2013.  In July 2012, the Company prepaid the outstanding balance of the note payable to Philip Isely.

 

Notes payable, related party consists of the following:

 
| ** **                                                 | ** ** | **As of September 30,** | ** ** |
|------------------------------------------------------------|------------|----------------------------------------|------------|
| ** **                                                 | ** ** | **2012**                               | ** ** | **2011** | ** ** |
| Margaret A. Isely Spouse’s Trust                      |       | $                                      | 282,499    |   | 529,210 |   |
| Philip Isely                                               |       | —                                 |       | 676,895 |   |
|                                                       |       | 282,499                                |       | 1,206,105 |   |
| Less current maturities                                    |       | (260,187                               | )          | (562,271 | ) |
| Notes payable—related party, net of current   portion |       | $                                      | 22,312     |   | 643,834 |   |

 

Principal maturities of $22,312 will be repaid during fiscal year 2013.

 

**12. Split-Dollar Life Insurance Premiums and Note Receivable—Related Party**

 

The Company had an agreement with a related party trust that owned a split-dollar life insurance policy dated January 1, 1994, on Philip Isely. One of the semiannual policy premium payments was paid by the Company each year. Split-dollar life insurance 

 

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premiums are reflected in long-term assets and represent the lesser of: (1) the cash surrender value of the policy; or (2) an amount equal to the total premiums paid by the Company. Split-dollar life insurance premiums were approximately $578,000 as of September 30, 2011, which represented premiums paid to date.

 

Additionally, the Company entered into a note receivable on August 16, 2004, with the co-trustees of the related party trust whereby the Company had agreed to pay the other semiannual policy premium due each policy year. The agreement stated that when the policy was paid, the Company would be repaid the premiums paid plus interest at 2.5% per annum. Amounts owed to the Company under this arrangement were approximately $266,000 at September 30, 2011.  The Company entered into a collateral assignment with the related party trust whereby the split-dollar life insurance policy is held as collateral security for its advances for premiums paid to date.

 

Section 402 of the Sarbanes-Oxley Act of 2002 was enacted to prohibit publicly traded companies from providing personal loans to directors and executive officers. As part of the Company’s process to initiate the IPO, it evaluated its arrangement with the related party trust that owns the life insurance policy and determined that it would be appropriate to extinguish the amounts receivable from the trust for the premiums paid by the Company on behalf of the trust. On June 14, 2012, the Company entered into an agreement with Zephyr Isely, Kemper Isely and Heather C. Isely, as co-trustees of The Philip and Margaret A. Isely Joint Trust Number One to terminate and cancel the split-dollar life insurance agreement, the collateral assignment, the loan agreement and related promissory note effective with the payment by the co-trustees/trust of all outstanding sums payable to the Company. As of June 14, 2012, the outstanding amounts were $659,852 for the premiums paid under the split-dollar life insurance agreement and $270,301 for the premiums paid and interest accrued per the loan agreement for a total receivable to the Company of $930,153. On June 15, 2012, the trust repaid this amount in full, and consistent with the original terms of the agreement, the Company has no further arrangements with the employee or the trust and no further obligations to pay the split-dollar life insurance policy premiums or any death benefit.

 

**13. Lease Commitments**

 

The Company leases retail stores, a bulk food repackaging facility and distribution center and administrative offices under long-term operating leases through 2028. These leases include scheduled increases in minimum rents and renewal provisions at the option of the Company. Deferred rent as of September 30, 2012 and 2011 was approximately $3.6 million and $2.8 million, respectively. Tenant improvement allowances received from landlords (leasehold incentives) are recorded as liabilities and recognized evenly as a reduction to rent expense over the lease term. Leasehold incentives at September 30, 2012 and 2011 were approximately $5.3 million and $4.9 million, respectively.

 

The Company has seven leases with Chalet Properties, LLC (Chalet), one lease with the Isely Family Land Trust LLC and one lease with 3801 East Second Avenue LLC, all related parties (see Note 16). The terms and rental rates of these related party leases are similar to leases with nonrelated parties and are at market rental rates. The leases began at various times with the earliest occurring in November 1999, continue for various terms through February 2027 and include various options to renew. Present monthly lease payments range from $4,000 to $38,000 per lease.

 

The minimum annual commitments under the terms of these operating leases as of September 30, 2012 are as follows:

 
| ** ** | ** ** | **Third   parties** | ** **  | **Related   parties** | ** ** | **Total Operating   Leases** | ** **  |
|------------|------------|---------------------|-------------|-----------------------|------------|-----------------------------------|-------------|
| 2013       |       | $                   | 11,024,540  |                  | 1,458,000  |                              | 12,482,540  |   |
| 2014       |       | 11,122,627          |        | 1,458,000             |       | 12,580,627                        |        |
| 2015       |       | 10,911,503          |        | 1,458,000             |       | 12,369,503                        |        |
| 2016       |       | 10,691,308          |        | 1,435,250             |       | 12,126,558                        |        |
| 2017       |       | 10,246,325          |        | 1,437,000             |       | 11,683,325                        |        |
| Thereafter |       | 65,510,218          |        | 12,476,250            |       | 77,986,468                        |        |
|       |       | $                   | 119,506,521 |                  | 19,722,500 |                              | 139,229,021 |   |

 

The Company recently entered into lease agreements with a developer for four build to suit store locations, two of which were new stores that were open as of September 30, 2012 and two of which were under construction as of September 30, 2012.  These leases expire or become subject to renewal clauses at various dates in fiscal years 2027 and 2028.  Under the terms of the lease agreements, the Company is responsible for contributing certain amounts towards the cost of construction.  As a result of this involvement, the Company was deemed the “owner” for accounting purposes during the construction period, and is required to capitalize the construction costs on its balance sheet.  Upon completion of the project, the Company performs a sale-leaseback analysis pursuant to ASC Topic 840, *Leases,*to determine if the Company can remove the assets from its balance sheet.  In accordance with the terms of the lease agreements, the Company is not reimbursed for the amounts contributed towards the cost of construction 

 

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and is therefore deemed to have “continuing involvement” per ASC Topic 840, *Leases*, which prevents the Company from derecognizing the assets on the balance sheet when construction is complete and requires the Company to account for the leases as capitalized real estate leases and related capital lease finance obligations.  As provided by ASC Topic 840, *Leases,*the Company records the fair market value of the building as an asset on its balance sheet, and records a capital lease finance obligation equal to the fair market value of the building less the amount the Company contributed towards construction.  The Company does not record rent expense for these leases, but rather rental payments per the lease agreements are recognized as a reduction of the capital lease finance obligation and as interest expense.

 

Two of the leases were for new stores that were open as of September 30, 2012.  The Company performed a sale-leaseback analysis upon completion of construction and was deemed to have continuing involvement which precluded the Company from removing the assets from its balance sheet.  Accordingly, the Company recorded approximately $5.2 million in assets and $4.2 million in capital lease finance obligations.

 

Future payments to the developer under the terms of the agreements for these two stores that were open as of September 30, 2012 are as follows at September 30, 2012:

 
| ** ** | ** ** | **Interest    expense on    capital lease    finance    obligations** | ** **      | **Principal    payments on    capital lease    finance    obligations** | ** ** | **Future    payments to    developer over    the term of the    agreement** | ** ** |
|------------|------------|-----------------------------------------------------------------------------------------------------|-----------------|-------------------------------------------------------------------------------------------------------|------------|--------------------------------------------------------------------------------------------------------------------------|------------|
| 2013       |       | $                                                                                                   |  652,847   |                                                                                                  | 11,884     |                                                                                                                     | 664,732    |   |
| 2014       |       | 651,018                                                                                             |            | 13,713                                                                                                |       | 664,731                                                                                                                  |       |
| 2015       |       | 648,891                                                                                             |            | 15,840                                                                                                |       | 664,731                                                                                                                  |       |
| 2016       |       | 646,417                                                                                             |            | 18,314                                                                                                |       | 664,731                                                                                                                  |       |
| 2017       |       | 643,534                                                                                             |            | 21,197                                                                                                |       | 664,731                                                                                                                  |       |
| Thereafter |       | 6,060,484                                                                                           |            | 627,905                                                                                               |       | 6,688,388                                                                                                                |       |
|       |       | $                                                                                                   |  9,303,191 |                                                                                                  | 708,853    |                                                                                                                     | 10,012,044 |   |

 

These two capital lease finance obligations have 15 year terms.  During the life of these leases, the Company will record approximately $9.3 million in interest expense and reduce the capital lease finance obligations by approximately $709,000.  At the end of these lease agreements, the Company will have assets of approximately $3.5 million, net of depreciation, and a capital lease finance obligation of approximately $3.5 million, both of which will be de-recognized at the end of the lease term.

 

The remaining two leases were for new stores that are scheduled to open in the first quarter of fiscal year 2013, for which the Company recorded approximately $1.9 million for construction in process and approximately $1.3 million in capital lease finance obligations.  Once construction is complete, the Company expects to be deemed to have continuing involvement and will capitalize the final costs of construction.  The Company will not record rent expense for these leases, but rather rental payments under the capital leases will be recognized as a reduction of the capital lease finance obligation and as interest expense, these amounts will be determinable upon completion of construction.  Future payments to the developer under the terms of these two locations that are in process where we are deemed to be the accounting owner during the construction period are as follows at September 30, 2012, based on the expected store opening date in the first quarter of fiscal 2013:

 
| ** ** | ** ** | **Future    payments to    developer over    the term of the    agreement** | ** **       |
|------------|------------|--------------------------------------------------------------------------------------------------------------------------|------------------|
| 2013       |       | $                                                                                                                        |  593,869    |   |
| 2014       |       | 680,585                                                                                                                  |             |
| 2015       |       | 680,585                                                                                                                  |             |
| 2016       |       | 680,585                                                                                                                  |             |
| 2017       |       | 680,585                                                                                                                  |             |
| Thereafter |       | 6,960,623                                                                                                                |             |
|       |       | $                                                                                                                        |  10,276,832 |   |

 

Total rent expense, including common area expenses and warehouse rent, for the years ended September 30, 2012, 2011 and 2010 totaled approximately $12.1 million, $9.9 million and $8.2 million, respectively, including approximately $519,000, $388,000 and $340,000 in pre-opening and relocation expenses associated with rent expense for stores that had not yet opened for the years ended September 30, 2012, 2011 and 2010, respectively.

 

20

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**14. Stockholders’ Equity**

 

*Dividends per Common Share*

 

The Company did not pay dividends during the years ended September 30, 2012, 2011 or 2010.

 

*Comprehensive Income*

 

Comprehensive income is comprised of net income and unrealized gains and losses on investments.  Comprehensive income included the following items for the periods presented:

 
| ** **                                                                 | ** ** | **Year ended September 30,** | ** ** |
|----------------------------------------------------------------------------|------------|---------------------------------------------|------------|
| ** **                                                                 | ** ** | **2012**                                    | ** ** | **2011** | ** ** |
| Net income attributable to Natural Grocers by   Vitamin Cottage, Inc. |       | $                                           | 6,648,800  |   | 3,503,811 |   |
| Unrealized loss on available-for-sale securities                           |       | (3,696                                      | )          | — |   |
| Comprehensive income                                                       |       | $                                           | 6,645,104  |   | 3,503,811 |   |

 

As of September 30, 2012, available-for-sale securities totaling approximately $1.8 million were in unrealized loss positions.

 

**15.  Stock-Based Compensation**

 

The Company adopted an Omnibus Incentive Plan (the Plan) on July 17, 2012. Stock awards granted pursuant to the Plan will be settled in new shares of the Company upon vesting. As of September 30, 2012, the Company had issued restricted stock unit awards to its Chief Financial Officer and a member of the Board of Directors which will be settled in shares of the Company’s common stock issued under the Plan once the awards are vested. The restricted stock grant to the Chief Financial Officer (CFO Award) was in accordance with the terms of her employment agreement that was signed in June 2008 which stated she was entitled to receive a grant of restricted stock units equal to 1.2% of the fully diluted shares of the Company in connection with an IPO.  Two thirds of the CFO Award vested immediately upon completion of the IPO and was settled in a combination of common stock and cash.  The remaining one third will be settled 100% in shares of common stock and vests in three equal parts over a six, 12 and 18 month period following the IPO.  Per ASC Topic 718, *Stock Compensation,* the occurrence of the IPO was deemed a performance condition, and therefore no expense was recorded until the performance condition was deemed probable (i.e. the closing of the IPO).  Upon completion of the IPO, the Company recorded the entire expense associated with the two thirds of the CFO Award that vested immediately, the portion that was settled in common shares was equity classified and expensed at the grant date fair value and the portion that was settled in cash was liability classified and expensed at the market value on the date of the IPO.  The grant date fair value was determined by a fair market value analysis of the Company performed by a third-party valuation specialist in fiscal year 2008.  The remaining one third of the CFO Award is valued at the grant date fair value, once the performance condition was deemed probable (occurrence of the IPO) a portion of the expense relating to the vesting period that had already expired (June 2008 to July 25, 2012) was expensed, and the remaining amount will be expensed ratably over the six, 12 and 18 month vesting period.

 

Each independent member of the Company’s Board of Directors is granted a number of restricted stock units under the Plan equal to the number of shares of common stock having a value of $50,000 (based on the closing price of common stock on the New York Stock Exchange on the date of grant), which is granted each year on the date of the Company’s annual meeting of stockholders, or a pro rata portion in the case of a mid-year appointment.  In July 2012, the Company appointed its first independent Board of Director member who received a restricted stock unit grant of 1,688 shares on August 1, 2012 with a grant date fair value of $19.74 which vests over a twelve month period.  Restricted common stock is granted at the market price of the stock on the day of grant, and is expensed over the applicable vesting period.

 

Total stock-based compensation expense before income taxes recognized in the year ended September 30, 2012 was approximately $1.1 million.  No stock-based compensation expense was recorded in the years ended September 30, 2011 or 2010. Stock-based compensation expense was included in the administrative expenses line item of the consolidated statements of income for the year ended September 30, 2012.

 

As of September 30, 2012, there was approximately $43,000 of unrecognized stock-based compensation expense related to nonvested restricted stock units related to approximately 90,909 shares with a weighted average grant date fair value of $1.66.  The Company anticipates that this expense will be recognized over a weighted average period of approximately one year.

 

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**16. Related Party Transactions**

 

The Company has ongoing relationships with several related entities:

 

*3801 East Second Avenue, LLC:*  The Company has one operating lease (see Note 13) for one of its store locations with 3801 East Second Avenue LLC, an entity owned by the estate of Philip Isely and the Margaret A. Isely Family Trust, with each holding a 50% interest in the entity.  The trust is controlled by Kemper Isely, Zephyr Isely and Heather Isely, who act as its trustees.  Rent paid to 3801 East Second Avenue LLC was approximately $48,000, $48,000 and $81,000 for the years ended September 30, 2012, 2011 and 2010, respectively.

 

*Isely Family Land Trust LLC:*  The Company has a lease for one of its store locations with the Isely Family Land Trust LLC (Land Trust). The Land Trust is owned by the Isely Children’s Trust and by the Margaret A. Isely Family Trust. Rent paid to the Land Trust was approximately $306,000 for each of the years ended September 30, 2012, 2011 and 2010, respectively.

 

*Chalet:*  The Company has seven store operating lease agreements with Chalet, a related party (see Note 13). Chalet is owned by four of the Company’s non-independent board members; Kemper Isely, Zephyr Isely, Heather Isely and Elizabeth Isely, and other related family members. Rent paid to Chalet was approximately $1.5 million, $1.2 million and $1.1 million for the years ended September 30, 2012, 2011 and 2010, respectively.

 

**17. Income Taxes**

 

The following are the components of the provision for income taxes as of September 30, 2012, 2011 and 2010, respectively:

 
| ** **                                   | ** ** | **Year ended September 30,** | ** ** |
|----------------------------------------------|------------|---------------------------------------------|------------|
| ** **                                   | ** ** | **2012**                                    | ** ** | **2011** | ** ** | **2010** | ** ** |
| Current federal income tax expense (benefit) |       | $                                           | 1,102,280  |   | (1,547,238 | ) | 1,657,441 |   |
| Current state income tax expense (benefit)   |       | 179,691                                     |       | (223,760 | ) | 212,223 |   |
|                                         |       | 1,281,971                                   |       | (1,770,998 | ) | 1,869,664 |   |
| Deferred federal income tax                  |       | 2,339,151                                   |       | 3,425,149 |   | 521,273 |   |
| Deferred state income tax                    |       | 334,097                                     |       | 512,649 |   | 74,835 |   |
|                                         |       | 2,673,248                                   |       | 3,937,798 |   | 596,108 |   |
| Total provision for income taxes             |       | $                                           | 3,955,219  |   | 2,166,800 |   | 2,465,772 |   |

 

The differences between the U.S. federal statutory income tax rate and the Company’s effective tax rate are as follows:

 
| ** **                                                  | ** ** | **Year ended September 30,** | ** ** |
|-------------------------------------------------------------|------------|---------------------------------------------|------------|
| ** **                                                  | ** ** | **2012**                                    | ** ** | **2011** | ** ** | **2010** | ** ** |
| Statutory tax rate                                          |       | 34.0                                        | %          | 34.0 |   | 34.0 |   |
| Nontaxable income attributable to noncontrolling   interest |       | (2.7                                        | )          | (6.2 | ) | (5.3 | ) |
| State income taxes, net of federal income tax   expense     |       | 3.0                                         |       | 3.4 |   | 2.5 |   |
| Other, net                                                  |       | 0.3                                         |       | 0.8 |   | (0.6 | ) |
| Effective tax rate                                          |       | 34.6                                        | %          | 32.0 |   | 30.6 |   |

 

Deferred taxes have been classified on the consolidated balance sheets as follows:

 
| ** **                   | ** ** | **As of September 30,** | ** ** |
|------------------------------|------------|----------------------------------------|------------|
| ** **                   | ** ** | **2012**                               | ** ** | **2011** | ** ** |
| Current assets               |       | $                                      | 842,963    |   | 583,668 |   |
| Long-term liabilities        |       | (4,143,351                             | )          | (4,947,870 | ) |
| Net deferred tax liabilities |       | $                                      | (3,300,388 | ) | (4,364,202 | ) |

 

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The tax effects of temporary differences that give rise to significant portions of deferred tax assets and deferred tax liabilities are as follows:

 
| ** **                           | ** ** | **As of September 30,** | ** ** |
|--------------------------------------|------------|----------------------------------------|------------|
| ** **                           | ** ** | **2012**                               | ** ** | **2011** | ** ** |
| Deferred tax assets                  |       |                                   |       |   |   |
| Trademarks                           |       | $                                      | 998,270    |   | 999,871 |   |
| Deferred rent                        |       | 1,343,691                              |       | 975,748 |   |
| Leasehold incentives                 |       | 1,978,421                              |       | 1,736,643 |   |
| Capital lease finance obligation     |       | 2,052,113                              |       | — |   |
| Accrued employee benefits            |       | 515,192                                |       | 414,800 |   |
| Intangible assets—other         |       | 87,782                                 |       | 96,265 |   |
| Goodwill and BVC related intangibles |       | 3,377,416                              |       | 11,662 |   |
| Charitable contribution              |       | —                                 |       | 46,818 |   |
| Other                                |       | 328,628                                |       | 122,050 |   |
| Gross deferred tax assets            |       | 10,681,513                             |       | 4,403,857 |   |
| Deferred tax liabilities             |       |                                   |       |   |   |
| Property and equipment               |       | (11,960,271                            | )          | (6,727,381 | ) |
| Leasehold improvements               |       | (2,012,131                             | )          | (1,763,365 | ) |
| Favorable operating lease            |       | (9,499                                 | )          | (34,737 | ) |
| Investment in BVC                    |       | —                                 |       | (242,576 | ) |
| Gross deferred tax liabilities       |       | (13,981,901                            | )          | (8,768,059 | ) |
| Net deferred tax liabilities         |       | $                                      | (3,300,388 | ) | (4,364,202 | ) |

 

Prior to the purchase of the noncontrolling interest in BVC in connection with the IPO, BVC was treated as a partnership under the Internal Revenue Code and similar state statutes; therefore, no provision or liability for federal or state income taxes related to the noncontrolling interest in BVC was included in the consolidated financial statements for the years ended September 30, 2011 and prior. The deferred tax amounts for the Company’s book versus tax basis in its 55% interest of BVC was reflected in the consolidated tax provision as outside basis in BVC for the years ended September 30, 2011 and prior.  Following the purchase of the noncontrolling interest in BVC, income from BVC is treated as taxable income to the Company and included in the provision for federal and state income taxes.  As a result of the acquisition of the remaining noncontrolling interest, the Company is entitled to tax deductions to the extent of any step up in tax basis on the assets of BVC, limited to the cash consideration paid.  Additionally, for tax purposes the Company recorded the noncontrolling interest purchase by stepping up acquired fixed asset balances by approximately $827,000 to reflect fair market value and recorded additional intangibles of approximately $9.2 million.  Accordingly, the tax basis in excess of book basis at the date of purchase resulted in deferred tax assets of approximately $3.6 million.

 

The Company believes that it is more likely than not that it will fully realize all deferred tax assets in the form of future deductions based on the nature of the deductible temporary differences and expected future taxable income.

 

As of September 30, 2012, the Company had $145,131 in operating loss carryforwards related to state income taxes.  The Company utilized $73,941 in state income tax carryforwards in the year ended September 30, 2012.

 

The Company files income tax returns with federal, state and local tax authorities. With limited exceptions, the Company is no longer subject to federal income tax examinations for fiscal years 2008 and prior and is no longer subject to state and local income tax examinations for fiscal years 2007 and prior.

 

The increase in deferred federal income taxes in fiscal year 2011 is the result of the 100% bonus depreciation legislation passed in fiscal year 2011, which provides that the Company may take a 100% bonus depreciation deduction for qualified property acquired or constructed and placed into service from September 8, 2010 through December 31, 2011.  Bonus depreciation was reduced to 50% for the period of January 1, 2012 through December 31, 2012.

 

**18. Defined Contribution Plan**

 

The Company has a defined contribution retirement plan (the Retirement Plan) covering substantially all employees who meet certain eligibility requirements as to age and length of service. The Retirement Plan incorporates the salary deferral provisions of Section 401(k) of the Internal Revenue Code. Employees may defer up to the annual maximum limit prescribed by the Internal Revenue Code. The Company, on a discretionary basis, matches 25% of participant contributions up to a maximum annual employer match of $2,500. The Company’s matching contribution included in expense was approximately $322,000, $260,000 and $232,000 for the years ended September 30, 2012, 2011 and 2010, respectively.

 

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**19. Segment Reporting**

 

The Company has one reporting segment, natural and organic retail stores. The Company’s revenues are derived from the sale of natural and organic products at its stores. All existing operations are domestic.

 

Sales from the Company’s natural and organic retail stores are derived from sales of the following products which are presented as a percentage of sales for the years ended September 30, 2012, 2011 and 2010 as follows:

 
| ** **          | ** ** | **As of September 30,** | ** ** |
|---------------------|------------|----------------------------------------|------------|
| ** **          | ** ** | **2012**                               | ** ** | **2011** | ** ** | **2010** | ** ** |
| Grocery             |       | 62.7                                   | %          | 59.8 |   | 57.6 |   |
| Dietary supplements |       | 27.0                                   |       | 29.3 |   | 31.3 |   |
| Other               |       | 10.3                                   |       | 10.9 |   | 11.1 |   |
|                |       | 100.0                                  | %          | 100.0 |   | 100.0 |   |

 

**20. Selected Quarterly Financial Data (Unaudited)**

 

The summarized quarterly financial data presented below reflect all adjustments, which in the opinion of management, are of a normal and recurring nature necessary to present fairly the results of operations for the periods presented.

 

Summarized unaudited quarterly financial data for fiscal year 2012 is as follows:

 
| ** **                                                                 | ** ** | **Three months ended** | ** ** |
|----------------------------------------------------------------------------|------------|----------------------------------|------------|
| ** **                                                                 | ** ** | **December 31,   2011**     | ** ** | **March 31,********2012** | ** ** | **June 30,********2012** | ** ** | **September 30,   2012** | ** ** |
| Net sales                                                                  |       | $                                | 74,838,619 |   | 84,907,259 |   | 86,706,603 |   | 89,932,891 |   |
| Cost of goods sold and occupancy costs                                     |       | 53,239,410                       |       | 59,223,589 |   | 61,306,972 |   | 63,558,793 |   |
| Gross profit                                                               |       | 21,599,209                       |       | 25,683,670 |   | 25,399,631 |   | 26,374,098 |   |
| Store expenses                                                             |       | 16,439,859                       |       | 18,028,062 |   | 18,198,873 |   | 19,490,337 |   |
| Administrative expenses                                                    |       | 2,712,670                        |       | 2,812,256 |   | 2,760,154 |   | 4,447,020 |   |
| Pre-opening and relocation expenses                                        |       | 426,903                          |       | 426,728 |   | 457,536 |   | 862,014 |   |
|                                                                       |       | 19,579,432                       |       | 21,267,046 |   | 21,416,563 |   | 24,799,371 |   |
| Operating income                                                           |       | 2,019,777                        |       | 4,416,624 |   | 3,983,068 |   | 1,574,727 |   |
| Other income (expense):                                                    |       |                             |       |   |   |   |   |   |   |
| Dividends and interest income                                              |       | 1,682                            |       | 2,329 |   | 1,427 |   | 658 |   |
| Interest expense                                                           |       | (175,199                         | )          | (154,928 | ) | (144,403 | ) | (93,971 | ) |
| Total other expense                                                        |       | (173,517                         | )          | (152,599 | ) | (142,976 | ) | (93,313 | ) |
| Income before income taxes                                                 |       | 1,846,260                        |       | 4,264,025 |   | 3,840,092 |   | 1,481,414 |   |
| Provision for income taxes                                                 |       | (586,262                         | )          | (1,486,443 | ) | (1,300,121 | ) | (582,393 | ) |
| Net income                                                                 |       | 1,259,998                        |       | 2,777,582 |   | 2,539,971 |   | 899,021 |   |
| Net (income) loss attributable to noncontrolling   interest                |       | (269,686                         | )          | (292,503 | ) | (339,178 | ) | 73,595 |   |
| Net income attributable to Natural Grocers by   Vitamin Cottage, Inc. |       | $                                | 990,312    |   | 2,485,079 |   | 2,200,793 |   | 972,616 |   |

 

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Summarized unaudited quarterly financial data for fiscal year 2011 is as follows:

 
| ** **                                                                 | ** ** | **Three months ended** | ** ** |
|----------------------------------------------------------------------------|------------|----------------------------------|------------|
| ** **                                                                 | ** ** | **December 31,   2010**     | ** ** | **March 31,   2011** | ** ** | **June 30,********2011** | ** ** | **September 30,   2011** | ** ** |
| Net sales                                                                  |       | $                                | 60,618,292 |   | 66,211,085 |   | 67,578,181 |   | 70,136,488 |   |
| Cost of goods sold and occupancy costs                                     |       | 42,961,018                       |       | 46,685,239 |   | 47,828,295 |   | 49,687,700 |   |
| Gross profit                                                               |       | 17,657,274                       |       | 19,525,846 |   | 19,749,886 |   | 20,448,788 |   |
| Store expenses                                                             |       | 13,221,010                       |       | 14,362,484 |   | 14,635,023 |   | 15,391,173 |   |
| Administrative expenses                                                    |       | 2,489,345                        |       | 2,602,642 |   | 2,574,890 |   | 2,730,014 |   |
| Pre-opening and relocation expenses                                        |       | 337,185                          |       | 685,422 |   | 446,930 |   | 494,649 |   |
|                                                                       |       | 16,047,540                       |       | 17,650,548 |   | 17,656,843 |   | 18,615,836 |   |
| Operating income                                                           |       | 1,609,734                        |       | 1,875,298 |   | 2,093,043 |   | 1,832,952 |   |
| Other income (expense):                                                    |       |                             |       |   |   |   |   |   |   |
| Dividends and interest income                                              |       | 5,257                            |       | 1,450 |   | 1,630 |   | 1,740 |   |
| Interest expense                                                           |       | (197,631                         | )          | (195,177 | ) | (181,470 | ) | (94,847 | ) |
| Other income, net                                                          |       | —                           |       | 16,069 |   | 1,837 |   | 6,801 |   |
| Total other expense                                                        |       | (192,374                         | )          | (177,658 | ) | (178,003 | ) | (86,306 | ) |
| Income before income taxes                                                 |       | 1,417,360                        |       | 1,697,640 |   | 1,915,040 |   | 1,746,646 |   |
| Provision for income taxes                                                 |       | (431,630                         | )          | (516,926 | ) | (674,782 | ) | (543,462 | ) |
| Net income                                                                 |       | 985,730                          |       | 1,180,714 |   | 1,240,258 |   | 1,203,184 |   |
| Net income attributable to noncontrolling interest                         |       | (259,354                         | )          | (307,306 | ) | (254,197 | ) | (285,218 | ) |
| Net income attributable to Natural Grocers by   Vitamin Cottage, Inc. |       | $                                | 726,376    |   | 873,408 |   | 986,061 |   | 917,966 |   |

 

**21. Commitments and Contingencies**

 

*Self-Insurance*

 

The Company is self-insured for claims under its health benefit plans, subject to a stop loss policy. The self-insurance liability related to claims under the Company’s health benefit plans is determined based on analysis of actual claims. The amounts related to these claims are included as a component of accrued benefits in accounts payable and accrued expenses. Liabilities associated with the risks that are retained by the Company are estimated, in part, by considering historical claims experience, demographic factors and other actuarial assumptions. While the Company believes that its assumptions are appropriate, the estimated accrual for these liabilities could be significantly affected if future occurrences and claims differ from these assumptions and historical trends.

 

*Legal*

 

The Company is periodically involved in various legal proceedings that are incidental to the conduct of its business, including but not limited to employment discrimination claims and customer injury claims. When the potential liability from a matter can be estimated and the loss is considered probable, the Company records the estimated loss. Due to uncertainties related to the resolution of lawsuits and claims, the ultimate outcome may differ from the estimates. Although the Company cannot predict with certainty the ultimate resolution of any lawsuits, investigations and claims asserted against it, management does not believe any currently pending legal proceeding to which the Company is a party will have a material adverse effect on its business, prospects, financial condition, cash flows or results of operations.

 

**22. Subsequent Events**

 

On October 17, 2012, the Board of Directors (Board) of the Company elected Richard Hallé as a new member of the Board.  As an independent director, Mr. Hallé will receive a base annual retainer of $30,000 in cash, and he will receive an additional annual retainer of $5,000 in cash as a member of the Audit Committee.  Mr. Hallé was granted 1,136 restricted stock units under the Company’s Omnibus Incentive Plan equal to the number of shares of the Company’s common stock having a value of $50,000 based on the closing price of the Company’s common stock on the day of the grant, October 17, 2012, on a pro-rata basis for Mr. Hallé’s service prior to the 2013 annual meeting.  The restricted stock units will fully vest on the date that is one year after the date of grant.

 

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**SIGNATURES**

 

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized on December 17, 2012.

 
|   | Natural   Grocers by Vitamin Cottage, Inc. |
|--------|-------------------------------------------------|
|   |                                            |   |
|   |                                            |   |
|   | By:                                             | /s/ Kemper Isely |
|   |                                            | Kemper Isely, |
|   |                                            | *Its Co-President* |

 

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons in the capacities and on the dates indicated.

 
| **Name**             | ** ** | **Title**                                      | ** ** | **Date**               |
|----------------------|------------|------------------------------------------------|------------|------------------------|
| ** **           | ** ** | ** **                                     | ** ** | ** **             |
| /s/ KEMPER ISELY     |       | (Principal   Executive Officer, Co-President,  |       |                   |
| Kemper Isely         |       | Director)                                      |       | December 17, 2012 |
|                 |       |                                           |       |                   |
|                 |       |                                           |       |                   |
| /s/ ZEPHYR ISELY     |       | (Principal   Executive Officer, Co-President,  |       |                   |
| Zephyr Isely         |       | Director)                                      |       | December 17, 2012 |
|                 |       |                                           |       |                   |
|                 |       |                                           |       |                   |
| /s/ SANDRA BUFFA     |       | (Principal   Financial and Accounting Officer) |       |                   |
| Sandra Buffa         |       |                                           |       | December 17, 2012 |
|                 |       |                                           |       |                   |
|                 |       |                                           |       |                   |
| /s/ HEATHER ISELY    |       | Director                                       |       |                   |
| Heather Isely        |       |                                           |       | December 17, 2012 |
|                 |       |                                           |       |                   |
|                 |       |                                           |       |                   |
| /s/ ELIZABETH ISELY  |       | Director                                       |       |                   |
| Elizabeth Isely      |       |                                           |       | December 17, 2012 |
|                 |       |                                           |       |                   |
|                 |       |                                           |       |                   |
| /s/ MICHAEL CAMPBELL |       | Director                                       |       |                   |
| Michael Campbell     |       |                                           |       | December 17, 2012 |
|                 |       |                                           |       |                   |
|                 |       |                                           |       |                   |
| /s/ RICHARD HALLE    |       | Director                                       |       |                   |
| Richard Halle        |       |                                           |       | December 17, 2012 |

 

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**EXHIBIT INDEX**

** **
| **Exhibit   Number** | ** ** | **Description**                                                                                                                                                                                                                                      | ** ** | **Form**      | ** ** | **File No.** | ** ** | **Exhibit   Number** | ** ** | **Filing Date** |
|----------------------|------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|---------------|------------|-------------------|------------|----------------------|------------|----------------------|
| 2.1                  |       | Limited Liability Company Interest   Purchase and Contribution Agreement between Vitamins, Inc., Howard &   Forey, Inc., Natural Grocers by Vitamin Cottage, Inc. and Vitamin   Cottage Natural Food Markets, Inc. dated June 14, 2012 |       | Form S-1 |       | 333-182186        |       | 2.1                  |       | June 29, 2012   |
| 2.2                  |       | Form of Agreement and Plan of Merger   by and among Vitamin Cottage Natural Food Markets, Inc., Vitamin Merger, Inc.   and Natural Grocers by Vitamin Cottage, Inc.                                                                                  |       | Form S-1 |       | 333-182186        |       | 2.2                  |       | July 12, 2012   |
| 3.1                  |       | Amended and Restated Certificate of   Incorporation                                                                                                                                                                                                  |       | Form S-1 |       | 333-182186        |       | 3.1                  |       | July 5, 2012    |
| 3.2                  |       | Amended and Restated Bylaws                                                                                                                                                                                                                          |       | Form S-1 |       | 333-182186        |       | 3.2                  |       | July 5, 2012    |
| 4.1                  |       | Reference is made to Exhibits 3.1 and   3.2                                                                                                                                                                                                          |       |          |       |              |       |                 |       |                 |
| 4.2                  |       | Specimen Common Stock Certificate                                                                                                                                                                                                                    |       | Form S-1 |       | 333-182186        |       | 4.2.                 |       | July 20, 2012   |
| 4.3                  |       | Form of Notice of Grant of Stock   Unit Award                                                                                                                                                                                                   |       | Form S-8 |       | 333-182886        |       | 4.2.                 |       | July 27, 2012   |
| 4.4                  |       | Form of Registration Rights Agreement                                                                                                                                                                                                                |       | Form S-1 |       | 333-182186        |       | 4.3                  |       | July 5, 2012    |
| 10.1                 |       | Amended and Restated Employment   Agreement by and between Vitamin Cottage Natural Food Markets, Inc., Natural   Grocers by Vitamin Cottage, Inc. and Sandra M. Buffa, dated June 26, 2012*                                                          |       | Form S-1 |       | 333-182186        |       | 10.1                 |       | June 29, 2012   |
| 10.2                 |       | Credit Agreement among Vitamin   Cottage Natural Food Markets, Inc., the Lenders Party thereto, and JPMorgan   Chase Bank, N.A., as Administrative Agent, dated September 29, 2006                                                              |       | Form S-1 |       | 333-182186        |       | 10.2                 |       | June 29, 2012   |
| 10.3                 |       | First Amendment to Credit Agreement   by and among Vitamin Cottage Natural Food Markets, Inc. and JPMorgan Chase   Bank, N.A., dated November 2, 2006                                                                                                |       | Form S-1 |       | 333-182186        |       | 10.3                 |       | June 29, 2012   |
| 10.4                 |       | Second Amendment to Credit Agreement   by and among Vitamin Cottage Natural Food Markets, Inc. and JPMorgan Chase   Bank, N.A., dated December 13, 2006                                                                                         |       | Form S-1 |       | 333-182186        |       | 10.4                 |       | June 29, 2012   |
| 10.5                 |       | Third Amendment to Credit Agreement   among Vitamin Cottage Natural Food Markets, Inc. the Lenders under the Credit   Agreement and JPMorgan Chase Bank, N.A., as Lender and Administrative Agent,   dated June 26, 2007                             |       | Form S-1 |       | 333-182186        |       | 10.5                 |       | June 29, 2012   |
| 10.6                 |       | Fourth Amendment to Credit Agreement   among Vitamin Cottage Natural Food Markets, Inc., the Lenders under the   Credit Agreement and JPMorgan Chase Bank, N.A., as Lender and Administrative   Agent, dated November 30, 2008                       |       | Form S-1 |       | 333-182186        |       | 10.6                 |       | June 29, 2012   |
| 10.7                 |       | Fifth Amendment to Credit Agreement   among Vitamin Cottage Natural Food Markets, Inc., the Lenders under the   Credit Agreement and JPMorgan Chase Bank, N.A., as Lender and Administrative   Agent,                                                |       | Form S-1 |       | 333-182186        |       | 10.7                 |       | June 29, 2012   |

 

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| **Exhibit   Number** | ** ** | **Description**                                                                                                                                                                                                                                | ** ** | **Form**      | ** ** | **File No.** | ** ** | **Exhibit   Number** | ** ** | **Filing Date** |
|----------------------|------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|---------------|------------|-------------------|------------|----------------------|------------|----------------------|
|                 |       | dated June 30, 2009                                                                                                                                                                                                                            |       |          |       |              |       |                 |       |                 |
| 10.8                 |       | Sixth Amendment to Credit Agreement   among Vitamin Cottage Natural Food Markets, Inc., the Lenders under the   Credit Agreement and JPMorgan Chase Bank, N.A., as Lender and Administrative   Agent, dated June 30, 2010                      |       | Form S-1 |       | 333-182186        |       | 10.8                 |       | June 29, 2012   |
| 10.9                 |       | Seventh Amendment to Credit Agreement   among Vitamin Cottage Natural Food Markets, Inc., the Lenders under the   Credit Agreement and JPMorgan Chase Bank, N.A., as Lender and Administrative   Agent, dated December 21, 2010           |       | Form S-1 |       | 333-182186        |       | 10.9                 |       | June 29, 2012   |
| 10.10                |       | Eighth Amendment to Credit Agreement   among Vitamin Cottage Natural Food Markets, Inc., the Lenders under the   Credit Agreement and JPMorgan Chase Bank, N.A., as Lender and Administrative   Agent, dated May 13, 2011                 |       | Form S-1 |       | 333-182186        |       | 10.10                |       | June 29, 2012   |
| 10.11                |       | Ninth Amendment to Credit Agreement   among Vitamin Cottage Natural Food Markets, Inc., the Lenders under the   Credit Agreement and JPMorgan Chase Bank, N.A., as Lender and Administrative   Agent, dated July 11, 2011                 |       | Form S-1 |       | 333-182186        |       | 10.11                |       | June 29, 2012   |
| 10.12                |       | Tenth Amendment to Credit Agreement   among Vitamin Cottage Natural Food Markets, Inc., the Lenders under the   Credit Agreement and JPMorgan Chase Bank, N.A., as Lender and Administrative   Agent, dated January 26, 2012                   |       | Form S-1 |       | 333-182186        |       | 10.12                |       | June 29, 2012   |
| 10.13                |       | Subordination Agreement by and among   Vitamin Cottage Two Ltd. Liability Company, and Vitamin Cottage Natural Food   Markets, Inc., in favor of JPMorgan Chase Bank, N.A., as administrative   agent, dated September 29, 2006           |       | Form S-1 |       | 333-182186        |       | 10.13                |       | June 29, 2012   |
| 10.14                |       | First Amendment to Subordination   Agreement by and between Vitamin Cottage Two Ltd. Liability Company, and   Vitamin Cottage Natural Food Markets, Inc., in favor of JPMorganChase Bank,   N.A., as administrative agent, dated June 26, 2007 |       | Form S-1 |       | 333-182186        |       | 10.14                |       | June 29, 2012   |
| 10.15                |       | Amended and Restated Promissory Note   by Vitamin Cottage Natural Food Markets, Inc., for the benefit of JPMorgan   Chase Bank, N.A., as Lender, dated December 21, 2010                                                                  |       | Form S-1 |       | 333-182186        |       | 10.15                |       | June 29, 2012   |
| 10.16                |       | Form of Omnibus Incentive Plan*                                                                                                                                                                                                                |       | Form S-1 |       | 333-182186        |       | 10.16                |       | July 5, 2012    |
| 10.17                |       | Summary of Compensation Arrangements   for Non-Employee Directors*                                                                                                                                                                             |       | Form S-1 |       | 333-182186        |       | 10.17                |       | June 29, 2012   |
| 10.18                |       | Form of Indemnification Agreement*                                                                                                                                                                                                             |       | Form S-1 |       | 333-182186        |       | 10.18                |       | June 29, 2012   |
| 10.19                |       | Shopping Center Lease by and between   Chalet Properties, LLC and Vitamin Cottage Natural Food Markets, Inc., dated                                                                                                                            |       | Form S-1 |       | 333-182186        |       | 10.19                |       | June 29, 2012   |

 

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| **Exhibit   Number** | ** ** | **Description**                                                                                                                                                | ** ** | **Form**      | ** ** | **File No.** | ** ** | **Exhibit   Number** | ** ** | **Filing Date** |
|----------------------|------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|---------------|------------|-------------------|------------|----------------------|------------|----------------------|
|                 |       | January 1, 2010                                                                                                                                                |       |          |       |              |       |                 |       |                 |
| 10.20                |       | Ground lease by and between 3801 East   Second Avenue, LLC and Vitamin Cottage Natural Food Markets, Inc., dated   March 1, 2001                               |       | Form S-1 |       | 333-182186        |       | 10.20                |       | June 29, 2012   |
| 10.21                |       | Commercial Lease by and between   Chalet Properties, LLC and Vitamin Cottage Natural Food Markets, Inc., dated   June 1, 2006                                  |       | Form S-1 |       | 333-182186        |       | 10.21                |       | July 5, 2012    |
| 10.22                |       | Sublease by and between Chalet   Properties, LLC and Vitamin Cottage Natural Food Markets, Inc., dated June 1,   2006                                          |       | Form S-1 |       | 333-182186        |       | 10.22                |       | June 29, 2012   |
| 10.23                |       | Lease by and between Chalet   Properties, LLC and Vitamin Cottage Natural Food Markets, Inc., dated   September 1, 2011                                   |       | Form S-1 |       | 333-182186        |       | 10.23                |       | June 29, 2012   |
| 10.24                |       | Lease by and between Chalet   Properties, LLC and Boulder Vitamin Cottage Group, LLC, dated July 1,   2011                                                |       | Form S-1 |       | 333-182186        |       | 10.24                |       | June 29, 2012   |
| 10.25                |       | Lease by and between Isely Family   Land Trust, LLC and Vitamin Cottage Natural Food Markets, Inc., dated   February 29, 2012                                  |       | Form S-1 |       | 333-182186        |       | 10.25                |       | June 29, 2012   |
| 10.26                |       | Lease by and between Chalet   Properties, Austin, LLC and Vitamin Cottage Natural Food Markets, Inc., dated   February 29, 2012                                |       | Form S-1 |       | 333-182186        |       | 10.26                |       | June 29, 2012   |
| 10.27                |       | Building Lease by and between Chalet Properties,   LLC and Vitamin Cottage Natural Food Markets, Inc., dated December 8,   2010                           |       | Form S-1 |       | 333-182186        |       | 10.27                |       | June 29, 2012   |
| 10.28                |       | Distribution Agreement between United   Natural Foods, Inc. and Vitamin Cottage Natural Food Markets, Inc., dated   May 20, 2008#                         |       | Form S-1 |       | 333-182186        |       | 10.28                |       | June 29, 2012   |
| 10.29                |       | Addendum A to Distribution Agreement   between United Natural Foods, Inc. and Vitamin Cottage Natural Food Markets,   Inc., dated February 27, 2009#           |       | Form S-1 |       | 333-182186        |       | 10.29                |       | June 29, 2012   |
| 10.30                |       | Agreement Addendum to Distribution   Agreement between United Natural Foods, Inc. and Vitamin Cottage Natural   Food Markets, Inc., dated March 10, 2012# |       | Form S-1 |       | 333-182186        |       | 10.30                |       | June 29, 2012   |
| 10.31                |       | Third Amendment to Distribution   Agreement between United Natural Foods, Inc. and Vitamin Cottage Natural Food   Markets, Inc., dated June 3, 2012#           |       | Form S-1 |       | 333-182186        |       | 10.31                |       | June 29, 2012   |
| 10.32                |       | Form of Stockholders Agreement, by,   between and among Natural Grocers by Vitamin Cottage, Inc. and the   stockholders to be named therein                    |       | Form S-1 |       | 333-182186        |       | 10.32                |       | July 12, 2012   |

 

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| **Exhibit   Number** | ** ** | **Description**                                                                                                                                                                                                                       | ** ** | **Form**  | ** ** | **File No.** | ** ** | **Exhibit   Number** | ** ** | **Filing Date** |
|----------------------|------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|-----------|------------|-------------------|------------|----------------------|------------|----------------------|
| 10.33                |       | Eleventh Amendment to Credit   Agreement among Vitamin Cottage Natural Food Markets, Inc., the Lenders under   the Credit Agreement and JPMorgan Chase Bank, N.A., as Lender and   Administrative Agent, dated October 31, 2012  |       | Form 10-K |       | 001-35608         |       | 10.33                |       | December 13, 2012    |
| 10.34                |       | Third Amended and Restated Promissory   Note by Vitamin Cottage Natural Food Markets, Inc., for the benefit of JPMorgan   Chase Bank, N.A., as Lender, dated October 31, 2012.                                                   |       | Form 10-K |       | 001-35608         |       | 10.34                |       | December 13, 2012    |
| 10.35                |       | Pledge and Security Agreement by and   between Natural Grocers by Vitamin Cottage, Inc. and JP Morgan Chase   Bank, N.A., as Administrative Agent, for the ratable benefit of the Secured   Parties, dated October 31, 2012 |       | Form 10-K |       | 001-35608         |       | 10.35                |       | December 13, 2012    |
| 10.36                |       | Guaranty made by Natural Grocers by   Vitamin Cottage, Inc. in favor of JP Morgan Chase Bank, N.A., as   Administrative Agent, for the ratable benefit of the Secured Parties, dated   October 31, 2012                     |       | Form 10-K |       | 001-35608         |       | 10.36                |       | December 13, 2012    |
| 14                   |       | Code of Ethics                                                                                                                                                                                                                        |       | Form 10-K |       | 001-35608         |       | 14                   |       | December 13, 2012    |
| 21.1                 |       | List of subsidiaries                                                                                                                                                                                                                  |       | Form 10-K |       | 001-35608         |       | 21.1                 |       | December 13, 2012    |
| 23.1                 |       | Consent of KPMG LLP                                                                                                                                                                                                                   |       | —    |       | —            |       | —               |       | —               |
| 31.1                 |       | Certification of Kemper Isely, a Principal Executive Officer Required   Under Section 302(a) of the Sarbanes-Oxley Act of 2002                                                                                              |       | —    |       | —            |       | —               |       | —               |
| 31.2                 |       | Certification of Zephyr Isely, a Principal Executive Officer Required   Under Section 302(a) of the Sarbanes-Oxley Act of 2002                                                                                              |       | —    |       | —            |       | —               |       | —               |
| 31.3                 |       | Certification of Sandra Buffa, Principal Financial Officer Required   Under Section 302(a) of the Sarbanes-Oxley Act of 2002                                                                                                |       | —    |       | —            |       | —               |       | —               |
| 32.1                 |       | Certification of Principal Executive Officers and Principal Financial   Officer Required Under 18 U.S.C. §1350, as adopted pursuant to   Section 906 of the Sarbanes-Oxley Act of 2002                                      |       | —    |       | —            |       | —               |       | —               |

 

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*Indicates a management contract or compensatory plan or arrangement

 

# Confidential portions have been omitted pursuant to a request for confidential treatment.

 

† The certifications attached as Exhibit 32.1 that accompany this Annual Report on Form 10-K, are not deemed filed with the Securities and Exchange Commission and are not to be incorporated by reference into any filing of Natural Grocers by Vitamin Cottage, Inc. under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended, whether made before or after the date of this Form 10-K, irrespective of any general incorporation language contained in such filing.

 

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