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| ☒ | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT OF 1934 |
|---------|--------------------------------------------------------------------------------------|

| ☐ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 |
|---------|------------------------------------------------------------------------------------------|

| Iowa                                                           |   | 20-1118105                        |
|----------------------------------------------------------------|--------|-----------------------------------|
| (State or other jurisdiction of incorporation or organization) |   | (IRS Employer Identification No.) |
| 59511 W. Lincoln Highway, Nevada, Iowa   |   | 50201      |
|------------------------------------------|--------|------------|
| (Address of principal executive offices) |   | (Zip Code) |

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| Large accelerated filer | ☐ | Accelerated filer         | ☐ |
|-------------------------|---------|---------------------------|---------|
| Non-accelerated filer   | ☑ | Smaller reporting company | ☐ |

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| Item 15. | Exhibits and Financial Statement Schedules. |
|----------|---------------------------------------------|

|   | (a)(3) | Exhibits. |
|--------|--------|-----------|

|  |   | The Exhibit Index attached to this report is incorporated by reference into this Item 15(a)(3). |
|--|--------|------------------------------------------------------------------------------------------------------|

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| January 4, 2017 | /s/ Eric Hakmiller                               |
|-----------------|-------------------------------------------------------|
|            | Eric Hakmiller, President and Chief Executive Officer |
|            |                                                  |
| January 4, 2017 | /s/ Kristine Strum                               |
|            | Kristine Strum, Director of Finance                   |

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|    |   |                                                                                                                                                |           | Incorporated by Reference |
|---------|--------|-----------------------------------------------------------------------------------------------------------------------------------------------------|----------------|---------------------------|
| Exhibit |   |                                                                                                                                                | Filed Herewith |                      | Period |   | Filing |
| Number  |   | Exhibit Description                                                                                                                                 |           | Form                      | Ending | Exhibit | Date |
| 3.1     |   | Restatement of the Certificate of Organization                                                                                                      |           | 10-K                      | 9/30/2010 | 3.1 | 12/21/2010 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 3.2     |   | Second Amended and Restated Operating Agreement and Unit Assignment Policy.                                                                         |           | 10-K                      | 9/30/2010 | 3.2 | 12/21/2010 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 3.2.1   |   | Amendment to Second Amended and Restated Operating Agreement                                                                                        |           | 8-K                       |   | 3.2.1 | 3/6/2013 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 3.2.2   |   | Second Amendment to Second Amended and Restated Operating Agreement                                                                                 | Filed Herewith |                      |   |   |   |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 10.1    |   | Distiller’s Grain Marketing Agreement Between Lincolnway Energy, LLC and Hawkeye Gold, LLC                                                    |           | 10-K                      | 9/30/2007 | 10.7 | 12/21/2007 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 10.1.1  |   | Amendment to Distiller’s Grains Marketing Agreement Between Lincolnway Energy, LLC and Hawkeye Gold, LLC                                      |           | 10-K                      | 9/30/2012 | 10.7.1 | 12/21/2012 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 10.2    |   | Industry Track Contract Between Lincolnway Energy, LLC and Union Pacific Railroad                                                                   |           | 10-Q                      | 6/30/2006 | 10.13 | 8/14/2006 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 10.3    |   | Master Loan Agreement and Amendment Among Farm Credit Services of America, FLCA; Farm Credit Services of America, PCA; and Lincolnway Energy, LLC   |           | 10-K                      | 9/30/2012 | 10.16 | 12/21/2012 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| *10.4   |   | Ethanol Marketing Agreement Between Lincolnway Energy, LLC and Eco-Energy, LLC                                                                      |           | 10-Q                      | 12/30/2012 | 10.19 | 2/14/2013 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| *10.5   |   | Coal Supply Agreement Between Lincolnway Energy, LLC and Williams Bulk Transfer, Inc.                                                               |           | 10-Q                      | 12/30/2012 | 10.20 | 2/14/2013 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 10.6    |   | Main Extension and Gas Transportation Agreement Between Lincolnway Energy, LLC and Interstate Power and Light Company                               |           | 10-Q                      | 3/31/2013 | 10.21 | 5/15/2013 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| **10.7  |   | Employment Agreement Between Lincolnway Energy, LLC and Eric Hakmiller                                                                              |           | 10-Q                      | 3/31/2013 | 10.22 | 5/15/2013 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 10.8    |   | Amendment to the Master Loan Agreement Among Farm Credit Services of America, FLCA, Farm Credit Services of America, PCA and Lincolnway Energy, LLC |           | 10-Q                      | 3/31/2013 | 10.23 | 5/15/2013 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| *10.9   |   | Distiller’s Grain Off-Take Agreement Between Lincolnway Energy, LLC and Gavilon Ingredients, LLC                                              |           | 10-K/A                    | 9/30/2013 | 10.27 | 4/23/2014 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 10.10   |   | Amendment to the Master Loan Agreement Among Farm Credit Services of America, FLCA, Farm Credit Services of America, PCA and Lincolnway Energy, LLC |           | 10-Q                      | 6/30/2014 | 10.28 | 8/13/2014 |
|    |   |                                                                                                                                                |           |                      |   |   |   |
| 10.11   |   | Amendment to the Master Loan Agreement Among Farm Credit Services of America, FLCA, Farm Credit Services of America, PCA and Lincolnway Energy, LLC |           | 10-Q                      | 6/30/2016 | 10.1 | 8/12/2016 |

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| 10.12       |   | Revolving Term Loan Supplement Between Farm Credit Services of America, FLCA and Lincolnway Energy, LLC dated June 2, 2016                                                                                                                                                                                                                                                                                                     | Filed Herewith |   |      |   |       |
|-------------|--------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------|--------|-----------|--------|------------|
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| 10.13       |   | Revolving Credit Supplement (Letter of Credit) Between Farm Credit Services of America, PCA and Lincolnway Energy, LLC dated June 2, 2016                                                                                                                                                                                                                                                                                      | Filed Herewith |   |      |   |       |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| 10.14       |   | Revolving Credit Supplement Between Farm Credit Services of America, PCA and Lincolnway Energy, LLC dated June 2, 2016                                                                                                                                                                                                                                                                                                         | Filed Herewith |   |      |   |       |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| *10.15      |   | Ethanol Marketing Agreement Between Lincolnway Energy, LLC and Eco-Energy, LLC                                                                                                                                                                                                                                                                                                                                                 |           | 8-K    |      | 10.1   | 12/9/2016  |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| 14          |   | Code of Ethics                                                                                                                                                                                                                                                                                                                                                                                                                 |           | 10-K   | 9/30/2009 | 14.0   | 12/22/2009 |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| 31.1        |   | Rule 13a-14(a) Certification of President and Chief Executive Officer                                                                                                                                                                                                                                                                                                                                                          |           | 10-K   | 9/30/2016 | 31.1   | 12/12/2016 |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| 31.1(A)     |   | Rule 13a-14(a) Certification of President and Chief Executive Officer                                                                                                                                                                                                                                                                                                                                                          | Filed Herewith |   |      |   |       |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| 31.2        |   | Rule 13a-14(a) Certification of Chief Financial Officer                                                                                                                                                                                                                                                                                                                                                                        |           | 10-K   | 9/30/2016 | 31.2   | 12/12/2016 |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| 31.2(A)     |   | Rule 13a-14(a) Certification of Chief Financial Officer                                                                                                                                                                                                                                                                                                                                                                        | Filed Herewith |   |      |   |       |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| †32.1 |   | Section 1350 Certification of President and Chief Executive Officer                                                                                                                                                                                                                                                                                                                                                            |           | 10-K   | 9/30/2016 | 31.2   | 12/12/2016 |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| †32.2 |   | Section 1350 Certification of Chief Financial Officer                                                                                                                                                                                                                                                                                                                                                                          |           | 10-K   | 9/30/2016 | 31.2   | 12/12/2016 |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| 101         |   | Interactive Data Files (furnished electronically herewith pursuant to Rule 405 of Regulation S-T)                                                                                                                                                                                                                                                                                                                              |           |   |      |   |       |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |           |   |      |   |       |
| *           |   | Material has been omitted pursuant to a request for confidential treatment and such material has been filed separately with the Securities and Exchange Commission.                                                                                                                                                                                                                                                            |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |
| **          |   | Management Contract or Compensatory Plan                                                                                                                                                                                                                                                                                                                                                                                       |
|        |   |                                                                                                                                                                                                                                                                                                                                                                                                                           |
| †     |   | This certification is not deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, or otherwise subject to the liability of that section. Such certification will not be deemed to be incorporated by reference into any filing under the Securities Act of 1933 or the Securities Exchange Act of 1934, except to the extent that the Company specifically incorporates it by reference. |

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