Document:

EX-10.3

 Exhibit 10.3 
 EXECUTION VERSION 
 SECOND AMENDMENT TO AMENDED AND RESTATED CREDIT AGREEMENT

 This SECOND AMENDMENT TO AMENDED AND RESTATED CREDIT AGREEMENT (this “Second Amendment”), dated as of
April 5, 2013, among Flowers Foods, Inc., a Georgia corporation (the “Borrower”), the Lenders party hereto, Deutsche Bank AG New York Branch, as administrative agent (the “Administrative Agent”), Swingline
Lender and Issuing Lender. Capitalized terms used herein and not otherwise defined herein shall have the meanings given to them in the Credit Agreement referred to below, as amended by this Second Amendment. References to Sections or Schedules are
references to Sections of, or Schedules to, the Credit Agreement, as applicable, unless otherwise stated. 
 RECITALS

 WHEREAS, the parties hereto are parties to a Credit Agreement, dated as of October 24, 2003, as amended and restated
as of October 29, 2004, as further amended and restated as of June 6, 2006, as further amended and restated as of May 20, 2011, and as amended as of November 16, 2012 (as so amended, and as further amended, amended and restated,
modified and/or supplemented to, but not including, the date hereof, the “Credit Agreement”), among the Borrower, the Lenders party thereto, the Administrative Agent, the Swingline Lender and Issuing Lender; and 

WHEREAS, the parties hereto desire to amend the Credit Agreement pursuant to the terms and conditions set forth herein. 

NOW, THEREFORE, in consideration of the premises and for other good and valuable consideration, the receipt of which is hereby
acknowledged, the parties hereto agree as follows: 
 1. Amendments and Agreements With Respect to the Credit Agreement.

 (i) Section 1.09 of the Credit Agreement is hereby amended by deleting the text “two,” immediately following
the text “at the option of the Borrower, be a one,”. 
 (ii) Section 4.04 of the Credit Agreement is hereby
restated in its entirety as follows: 
 “4.04 Net Payments; Taxes. 

(a) All payments made by any Credit Party hereunder or under any Note will be made without setoff, counterclaim or other defense. Except
as provided in Section 4.04(b), 13.04, 13.14 or 13.15 and except as required by applicable law, all such payments will be made free and clear of, and without deduction or withholding for, any present or future Taxes now or hereafter imposed by
any jurisdiction or by any political subdivision or taxing authority thereof or therein with respect to such payments (but excluding, except as provided in the second succeeding sentence, any Excluded Taxes) (all such non-excluded Taxes being
referred to collectively as “Withholding Taxes”). If any Withholding Taxes are so levied or imposed, the 

 
Borrower agrees to pay the full amount of such Withholding Taxes, and such additional amounts as may be necessary so that every payment of all amounts due under this Agreement or any other Credit
Document or under any Note, after withholding or deduction for or on account of any Withholding Taxes, will not be less than the amount provided for herein or in such Credit Document or in such Note. If any amounts are payable in respect of
Withholding Taxes pursuant to the preceding sentence, the Borrower agrees to reimburse each Lender, upon the written request of such Lender, for taxes imposed on or measured by the net income (however denominated) of the applicable Lender as a
result of such Lender being organized under the laws of, or having its principal office or its applicable lending office located in, the jurisdiction imposing such Tax (or any political subdivision thereof) and for any withholding of taxes as such
Lender shall determine are payable by, or withheld from, such Lender, in respect of such amounts so paid to or on behalf of such Lender pursuant to the preceding sentence and in respect of any amounts paid to or on behalf of such Lender pursuant to
this sentence. The Borrower will furnish to the Administrative Agent within 45 days after the date the payment of any Withholding Taxes is due pursuant to applicable law certified copies of tax receipts evidencing such payment by the Borrower. The
Borrower agrees to indemnify and hold harmless each Lender, and reimburse such Lender upon its written request, for the amount of any Withholding Taxes so levied or imposed and paid by such Lender. 

(b) (i) Any Lender that is entitled to an exemption from or reduction of Withholding Tax with respect to payments made under any Credit
Document shall deliver to the Borrower and the Administrative Agent, at the time or times reasonably requested by the Borrower or the Administrative Agent, such properly completed and executed documentation reasonably requested by the Borrower or
the Administrative Agent as will permit such payments to be made without withholding or at a reduced rate of withholding. In addition, any Lender, if reasonably requested by the Borrower or the Administrative Agent, shall deliver such other
documentation prescribed by applicable law or reasonably requested by the Borrower or the Administrative Agent as will enable the Borrower or the Administrative Agent to determine whether or not such Lender is subject to backup withholding or
information reporting requirements. Notwithstanding anything to the contrary in the preceding two sentences, the completion, execution and submission of such documentation (other than such documentation set forth in Section 4.04(b)(ii)(A),
(ii)(B) and (ii)(D) below) shall not be required if in the Lender’s reasonable judgment such completion, execution or submission would subject such Lender to any material unreimbursed cost or expense or would materially prejudice the legal or
commercial position of such Lender. 
 (ii) Without limiting the generality of the foregoing, in the event that the Borrower is
a U.S. Borrower, 
 (A) any Lender that is a U.S. Person shall deliver to the Borrower and the Administrative Agent on or prior
to the date on which such Lender becomes a Lender under this Agreement (and from time to time thereafter upon the reasonable request of the Borrower or the Administrative Agent), executed originals of IRS Form W-9 certifying that such Lender is
exempt from U.S. federal backup Withholding Tax; 

  
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 (B) any Foreign Lender shall, to the extent it is legally entitled to do so, deliver to the
Borrower and the Administrative Agent (in such number of copies as shall be requested by the recipient) on or prior to the date on which such Foreign Lender becomes a Lender under this Agreement (and from time to time thereafter upon the reasonable
request of the Borrower or the Administrative Agent), whichever of the following is applicable: 
 (i) in the
case of a Foreign Lender claiming the benefits of an income tax treaty to which the United States is a party (x) with respect to payments of interest under any Credit Document, executed originals of IRS Form W-8BEN establishing an exemption
from, or reduction of, U.S. federal Withholding Tax pursuant to the “interest” article of such tax treaty and (y) with respect to any other applicable payments under any Loan Document, IRS Form W-8BEN establishing an exemption from,
or reduction of, U.S. federal Withholding Tax pursuant to the “business profits” or “other income” article of such tax treaty; 
 (ii) executed originals of IRS Form W-8ECI; 
 (iii) in the case of
a Foreign Lender claiming the benefits of the exemption for portfolio interest under Section 881(c) of the Code, (x) a certificate substantially in the form of Exhibit D-1 to the effect that such Foreign Lender is not a “bank”
within the meaning of Section 881(c)(3)(A) of the Code, a “10 percent shareholder” of the Borrower within the meaning of Section 881(c)(3)(B) of the Code, or a “controlled foreign corporation” described in
Section 881(c)(3)(C) of the Code (a “U.S. Tax Compliance Certificate”) and (y) executed originals of IRS Form W-8BEN; or 
 (iv) to the extent a Foreign Lender is not the beneficial owner, executed originals of IRS Form W-8IMY, accompanied by IRS Form W-8ECI, IRS Form W-8BEN, a U.S. Tax Compliance Certificate substantially in
the form of Exhibit D-2 or Exhibit D-3, IRS Form W-9, and/or other certification documents from each beneficial owner, as applicable; provided that if the Foreign Lender is a partnership and one or more direct or indirect partners of such Foreign
Lender are claiming the portfolio interest exemption, such Foreign Lender may provide a U.S. Tax Compliance Certificate substantially in the form of Exhibit D-4 on behalf of each such direct and indirect partner; 

(C) any Foreign Lender shall, to the extent it is legally entitled to do so, deliver to the Borrower and the Administrative Agent (in
such number of copies as shall be requested by the recipient) on or prior to the date on which such Foreign Lender becomes a Lender under this Agreement (and from time to time thereafter upon the reasonable request of the Borrower or the
Administrative Agent), executed originals of any other form prescribed by applicable law as a basis for claiming exemption from or a reduction in U.S. federal Withholding Tax, duly completed, together with such supplementary documentation as may be
prescribed by applicable law to permit the Borrower or the Administrative Agent to determine the withholding or deduction required to be made; and 

  
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 (D) if a payment made to a Lender under any Credit Document would be subject to U.S. federal
Withholding Tax imposed by FATCA if such Lender were to fail to comply with the applicable reporting requirements of FATCA (including those contained in Section 1471(b) or 1472(b) of the Code, as applicable), such Lender shall deliver to the
Borrower and the Administrative Agent at the time or times prescribed by law and at such time or times reasonably requested by the Borrower or the Administrative Agent such documentation prescribed by applicable law (including as prescribed by
Section 1471(b)(3)(C)(i) of the Code) and such additional documentation reasonably requested by the Borrower or the Administrative Agent as may be necessary for the Borrower and the Administrative Agent to comply with their obligations under
FATCA and to determine that such Lender has complied with such Lender’s obligations under FATCA or to determine the amount to deduct and withhold from such payment. Solely for purposes of this clause (D), “FATCA” shall include any
amendments made to FATCA after the date of this Agreement. 
 Each Lender agrees that if any form or certification it previously
delivered expires or becomes obsolete or inaccurate in any respect, it shall update such form or certification or promptly notify the Borrower and the Administrative Agent in writing of its legal inability to do so. 

(c) If any party determines, in its sole discretion exercised in good faith, that it has received a refund of any Taxes as to which it
has been indemnified pursuant to this Section 4.04 (including by the payment of additional amounts pursuant to this Section 4.04), it shall pay to the indemnifying party an amount equal to such refund (but only to the extent of indemnity
payments made under this Section with respect to the Taxes giving rise to such refund), net of all out-of-pocket expenses (including Taxes) of such indemnified party and without interest (other than any interest paid by the relevant governmental
authority with respect to such refund). Such indemnifying party, upon the request of such indemnified party, shall repay to such indemnified party the amount paid over pursuant to this paragraph (c) (plus any penalties, interest or other
charges imposed by the relevant governmental authority) in the event that such indemnified party is required to repay such refund to such governmental authority. Notwithstanding anything to the contrary in this paragraph (c), in no event will the
indemnified party be required to pay any amount to an indemnifying party pursuant to this paragraph (c) the payment of which would place the indemnified party in a less favorable net after-Tax position than the indemnified party would have been
in if the Tax subject to indemnification and giving rise to such refund had not been deducted, withheld or otherwise imposed and the indemnification payments or additional amounts with respect to such Tax had never been paid. This paragraph shall
not be construed to require any indemnified party to make available its Tax returns (or any other information relating to its Taxes that it deems confidential) to the indemnifying party or any other Person.” 

(iii) Section 5.07 of the Credit Agreement is hereby amended by deleting the text “2,000,000” appearing therein and
inserting the text “5,000,000” in lieu thereof. 
 (iv) Section 7.10(a) of the Credit Agreement is hereby
restated in its entirety as follows: 
 “(a) (i) Each Plan is in compliance in all material respects with ERISA and
the Code; no Reportable Event has occurred with respect to a Plan; to the knowledge of the Borrower, no Multiemployer Plan is insolvent or in reorganization; no Plan has an Unfunded Current Liability; no Plan has an accumulated or waived funding
deficiency, or has applied for an extension of any amortization period within the meaning of Section 412 of the Code; neither 

  
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the Borrower nor any of its respective Subsidiaries nor any ERISA Affiliate has incurred any liability (other than contributions by the Borrower or an ERISA Affiliate timely made in accordance
with minimum funding requirements under Section 412 of the Code and in accordance with the requirements of Section 515 of ERISA) to or on account of a Plan and/or a Multiemployer Plan pursuant to Section 515, 4062, 4063, 4064, 4069,
4201, 4204 or 4212 of ERISA; no proceedings have been instituted to terminate or appoint a trustee to administer any Plan; no action, suit, proceeding, hearing, audit or investigation with respect to the administration, operation or investment of
assets of any Plan (other than routine claims for benefits) is pending, expected or threatened in writing; none of the Borrower, any of its respective Subsidiaries or any ERISA Affiliate has incurred a complete or partial withdrawal from any
Multiemployer Plan; (ii) and in each case in clause (a)(i) above, no liability, individually, or in the aggregate, has had or could reasonably be expected to have a Material Adverse Effect.” 

(v) Section 7.12 of the Credit Agreement is hereby restated in its entirety as follows: 

“7.12 [Reserved].” 
 (vi) Section 7.15 of the Credit Agreement is hereby restated in its entirety as follows: 
 “7.15 Anti-Terrorism Law. 
 (a) Neither the Borrower nor any of its
Subsidiaries is in violation of any legal requirement relating to any laws with respect to terrorism or money laundering (“Anti-Terrorism Laws”), including Executive Order No. 13224 on Terrorist Financing effective
September 24, 2001 (the “Executive Order”) and the USA Patriot Act. Neither the Borrower nor any of its Subsidiaries and, to the knowledge of the Borrower, no agent of the Borrower or any of its Subsidiaries acting on behalf of
the Borrower or any of its Subsidiaries, as the case may be, is any of the following: 
 (i) a Person that is
listed in the annex to, or is otherwise subject to the provisions of, the Executive Order; 
 (ii) a Person owned
or controlled by, or acting for or on behalf of, any Person that is listed in the annex to, or is otherwise subject to the provisions of, the Executive Order; 
 (iii) a Person with which any Lender is prohibited from dealing or otherwise engaging in any transaction by any Anti-Terrorism Law; 

(iv) a Person that commits, threatens or conspires to commit or supports “terrorism” as defined in the Executive
Order; or 
 (v) a Person that is named as a “specially designated national and blocked person” on the
most current list published by the U.S. Treasury Department Office of Foreign Assets Control (“OFAC”) at its official website or any replacement website or other replacement official publication of such list. 

  
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 (b) Neither the Borrower nor any of its Subsidiaries and, to the knowledge of the Borrower,
no agent of the Borrower or any of its Subsidiaries acting on behalf of the Borrower or any of its respective Subsidiaries, as the case may be, (i) conducts any business or engages in making or receiving any contribution of funds, goods or
services to or for the benefit of a Person described in Section 7.15(a), (ii) deals in, or otherwise engages in any transaction relating to, any property or interests in property blocked pursuant to the Executive Order, or
(iii) engages in or conspires to engage in any transaction that evades or avoids, or has the purpose of evading or avoiding, or attempts to violate, any of the prohibitions set forth in any Anti-Terrorism Law.” 

(vii) Section 7.19 of the Credit Agreement is hereby amended by deleting the text “2,000,000” appearing therein and
inserting the text “5,000,000” in lieu thereof. 
 (viii) Section 8.01(c) of the Credit Agreement is hereby
restated in its entirety as follows: 
 “(c) Officer’s Certificates. At the time of the delivery of the
financial statements provided for in Section 8.01(a) and (b), a certificate of an Authorized Representative of the Borrower in the form of Exhibit J to the effect that, to the best of such Authorized Representative’s knowledge, no Default
or Event of Default has occurred and is continuing or, if any Default or Event of Default has occurred and is continuing, specifying the nature and extent thereof, which certificate shall set forth the calculations required to establish whether the
Borrower was in compliance with the provisions of Sections 9.01(xiii), 9.05(v), 9.07 and 9.08 at the end of such fiscal quarter or year, as the case may be.” 
 (ix) Section 8.07 of the Credit Agreement is hereby amended by (x) inserting the parenthetical “(other than contributions by the Borrower or an ERISA Affiliate timely made in accordance
with minimum funding requirements under Section 412 of the Code and in accordance with the requirements of Section 515 of ERISA)” immediately after the text “incur any liability” and immediately before the text
“(including any indirect,” appearing in clause (vii) thereof, (y) deleting the text “Plan and/or Multiemployer” immediately after the text “4212 of ERISA or with respect to a” appearing therein and
(z) deleting the text “Affect” at the end of such Section and inserting the text “Effect” in lieu thereof. 
 (x) Section 8.10(a) of the Credit Agreement is hereby amended by (x) deleting the text “to the Administrative Agent” immediately after the text “deliver a Subsidiaries
Guaranty” appearing therein and (y) inserting the text “to the Administrative Agent (i) a schedule that sets forth the correct legal name of each Subsidiary of the Borrower, the direct and indirect (if any) owner of each such
Subsidiary and whether each such Subsidiary is a Wholly-Owned Domestic Subsidiary and (ii)” immediately after the text “such event) deliver”. 
 (xi) Section 9.01(xii) of the Credit Agreement is hereby amended by deleting the text “200,000,000” appearing therein and inserting the text “275,000,000” in lieu thereof.

  
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 (xii) Section 9.01(xiii) of the Credit Agreement is hereby amended by deleting the text
“150,000,000” appearing therein and inserting the text “200,000,000” in lieu thereof. 
 (xiii)
Section 9.01(xiii) of the Credit Agreement is hereby amended by deleting the text “180,000,000” appearing therein and inserting the text “225,000,000” in lieu thereof. 

(xiv) Section 9.07 of the Credit Agreement is hereby amended by inserting the following new text at the end of such Section:

 “; provided that, if the Borrowing Date (as defined in the 2013 Credit Agreement) occurs, the Borrower will not
permit the Leverage Ratio as of the last day of any fiscal quarter (x) following the Borrowing Date (as defined in the 2013 Credit Agreement), up to and including the last day of the fourth full fiscal quarter following the Borrowing Date (as
defined in the 2013 Credit Agreement), to be greater than 3.75:1.00 and (y) thereafter, to be greater than 3.50:1.00”. 
 (xv) Section 10.04 of the Credit Agreement is hereby amended by deleting the text “50,000,000” appearing therein and inserting the text “75,000,000” in lieu thereof. 

(xvi) Section 10.06 of the Credit Agreement is hereby restated in its entirety as follows: 

“Section 10.06 ERISA. (a) Any Plan and/or Multiemployer Plan shall fail to satisfy the minimum funding standard required
for any plan year or part thereof or a waiver of such standard or extension of any amortization period is sought or granted under Section 412 of the Code, any Plan and/or Multiemployer Plan shall have had or is likely to have a trustee
appointed to administer such Plan and/or Multiemployer Plan pursuant to Section 4042 of ERISA, any Plan and/or Multiemployer Plan shall have been or is reasonably expected to be terminated or to be the subject of termination proceedings under
Section 4042 of ERISA, any Plan and/or Multiemployer Plan shall have an Unfunded Current Liability, a contribution required to be made to a Plan, Multiemployer Plan and/or Foreign Pension Plan has not been timely made, or the Borrower or any of
its respective Subsidiaries or any ERISA Affiliate have incurred or is reasonably expected to incur a liability (other than contributions by the Borrower or an ERISA Affiliate timely made in accordance with minimum funding requirements under
Section 412 of the Code and in accordance with the requirements of Section 515 of ERISA) to or on account of a Plan and/or Multiemployer Plan under Section 409, 502(i), 502(l), 515, 4062, 4063, 4064, 4069, 4201, 4204 or 4212 of ERISA
or Section 401(a)(29), 4971, 4975 or 4980 of the Code; (b) there shall result from any such event or events the imposition of a lien, the granting of a security interest or a liability; (c) and in each case in clauses (a) and
(b) above, the same, individually or in the aggregate, has had or could reasonably be expected to have a Material Adverse Effect; or” 
 (xvii) Section 10.08 of the Credit Agreement is hereby amended by deleting the test “50,000,000” appearing therein and inserting the text “75,000,000” in lieu thereof. 

(xviii) The definition of “ERISA Affiliate” appearing in Section 11 of the Credit Agreement is hereby restated in its
entirety as follows: 

  
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 ““ERISA Affiliate” shall mean each person (as defined in
Section 3(9) of ERISA) which together with the Borrower or any Subsidiary of the Borrower would be deemed to be a “single employer” within the meaning of Section 414(b), (c), (m) or (o) of the Code.” 

(xix) The definition of “FATCA” appearing in Section 11 of the Credit Agreement is hereby restated in its entirety as
follows: 
 ““FATCA” shall mean Sections 1471 through 1474 of the Code, as of the date of this Agreement
(or any amended or successor version that is substantively comparable and not materially more onerous to comply with) and any current or future regulations or official interpretations thereof.” 

(xx) The definition of “Guaranteed Obligations” appearing in Section 11 of the Credit Agreement is hereby amended by
inserting the following new text at the end of such definition: 
 “; provided that, Guaranteed Obligations shall
exclude any Excluded Swap Obligations.” 
 (xxi) The definition of “Notice Office” appearing in Section 11
of the Credit Agreement is hereby restated in its entirety as follows: 
 ““Notice Office” shall mean the
office of the Administrative Agent located at 5022 Gate Parkway, Building 200, Jacksonville, Florida 32256, Attention: Lee Scherin (tele: (904) 520-5353) or such other office as the Administrative Agent may hereafter designate in writing as
such to the other parties hereto.” 
 (xxii) The definition of “Permitted Securitization” appearing in
Section 11 of the Credit Agreement is hereby restated in its entirety as follows: 
 ““Permitted
Securitization” shall mean any transaction or series of transactions that may be entered into by the Borrower or any Subsidiary of the Borrower pursuant to which it may sell, convey, contribute to capital or otherwise transfer (which sale,
conveyance, contribution to capital or transfer may include or be supported by the grant of a security interest) Receivables or interests therein and collateral securing such Receivables, contracts and contract rights, purchase orders, security
interests, financing statements or other documentation in respect of such Receivables, any guarantees, indemnities, warranties or other obligations or supporting obligations in respect of such Receivables, any other assets that are customarily
transferred or in respect of which security interests are customarily granted in connection with asset securitization transactions involving receivables similar to such Receivables and collections or proceeds of any of the foregoing (collectively,
the “Related Assets”) (i) to a trust, partnership, corporation or other Person (other than the Borrower or any Subsidiary of the Borrower other than a special purpose entity created primarily for the purposes of such transaction or
transactions), which transfer is funded in whole or in part, directly or indirectly, by the incurrence or issuance by the transferee or any successor transferee of Indebtedness or fractional undivided interests or other securities that are to
receive payments from, or that represent interests in, the cash flow derived from such Receivables and Related Assets or interests in such Receivables and Related Assets, or (ii) directly to one or more investors or other purchasers (other than
the Borrower or any Subsidiary of the Borrower other than a special purpose entity primarily created for purposes of 

  
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such transaction or transactions), it being understood that a Permitted Securitization may involve (A) one or more sequential transfers or pledges of the same Receivables and Related Assets,
or interests therein, and all such transfers, pledges and Indebtedness incurrences shall be part of and constitute a single Permitted Securitization, and (B) periodic transfers or pledges of Receivables and/or revolving transactions in which
new Receivables and Related Assets, or interests therein, are transferred or pledged upon collection of previously transferred or pledged Receivables and Related Assets, or interests therein; provided that (x) any such transactions shall
provide for recourse to such Subsidiary of the Borrower or the Borrower (as applicable) only in respect of the cash flows in respect of such Receivables and Related Assets and to the extent of other customary securitization undertakings in the
jurisdiction relevant to such transactions and (y) the aggregate amount of all such transactions constituting “Permitted Securitizations” shall not exceed an aggregate amount equal to $200,000,000 at any time outstanding. The
“amount” or “principal amount” of any Permitted Securitization shall be deemed at any time to be (1) the aggregate principal, or stated amount, of the Indebtedness or fractional undivided interests (which stated amount may
be described as a “net investment” or similar term reflecting the amount invested in such undivided interest) or other securities incurred or issued pursuant to such Permitted Securitization, in each case outstanding at such time, or
(2) in the case of any Permitted Securitization in respect of which no such Indebtedness, fractional undivided interests or securities are incurred or issued, the cash purchase price paid by the transferee in connection with its purchase of
Receivables less the amount of collections received by the Borrower or any Subsidiary of the Borrower in respect of such Receivables and paid to such transferee, in each case excluding any amounts applied to purchase fees or discount or in the
nature of interest and the aggregate principal amount or stated amount of Indebtedness, fractional undivided interests or other securities held by the Borrower, such Subsidiary or any Affiliate.” 

(xxiii) The definition of “Permitted Subsidiary Indebtedness” appearing in Section 11 of the Credit Agreement is hereby
amended by (a) deleting the text “1,000,000” appearing therein and inserting the text “5,000,000” in lieu thereof and (b) deleting the text “150,000,000” appearing therein and inserting the text
“200,000,000” in lieu thereof. 
 (xxiv) The definition of “Significant Acquisition” appearing in
Section 11 of the Credit Agreement is hereby amended by deleting the text “325,000,000” appearing therein and inserting the text “400,000,000” appearing therein. 

(xxv) The definition of “Unfunded Current Liability” appearing in Section 11 of the Credit Agreement is hereby restated in
its entirety as follows: 
 ““Unfunded Current Liability” of any Plan means the amount, if any, by which
the actuarial present value of the accumulated benefits under the Plan as of the close of its most recent plan year each exceeds the value of the assets allocable thereto, each determined in accordance with the funding requirements set forth under
Section 412 of the Code, based upon the actuarial assumptions used by the Plan’s actuary in the most recent annual valuation of the Plan.” 
 (xxvi) Section 11 of the Credit Agreement is hereby amended by adding the following new definitions in the appropriate alphabetical: 

  
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 “2013 Credit Agreement” shall mean that certain Credit Agreement, dated as
of April 5, 2013, among the Borrower, the lenders party thereto from time to time, Branch Banking and Trust Company, Coöperatieve Centrale Raiffeisen-Boerenleenbank B.A., “Rabobank Nederland”, New York Branch, and Regions Bank,
as co-documentation agents, Bank of America, N.A., as syndication agent, and Deutsche Bank AG New York Branch, as administrative agent. 
 “Anti-Terrorism Laws” shall have the meaning provided in Section 7.15(a). 
 “Commodity Exchange Act” shall mean the Commodity Exchange Act (7 U.S.C. § 1 et seq.). 
 “Excluded Swap Obligation” shall mean, with respect to any Subsidiary Guarantor (if any), any Swap Obligation if, and to the extent that, all or a portion of the Subsidiaries Guaranty of
such Subsidiary Guarantor of, or the grant by such Subsidiary Guarantor of a Lien to secure, such Swap Obligation (or any Subsidiaries Guaranty thereof) is or becomes illegal under the Commodity Exchange Act or any rule, regulation or order of the
Commodity Futures Trading Commission (or the application or official interpretation of any thereof) by virtue of such Subsidiary Guarantor’s failure for any reason to constitute an “eligible contract participant” as defined in the
Commodity Exchange Act and the regulations thereunder at the time the Subsidiaries Guaranty of such Subsidiary Guarantor or the grant of such security interest becomes effective with respect to such Swap Obligation. If a Swap Obligation arises under
a master agreement governing more than one swap, such exclusion shall apply only to the portion of such Swap Obligation that is attributable to swaps for which such Subsidiaries Guaranty or security interest is or becomes illegal. 

“Excluded Taxes” shall mean any of the following Taxes imposed on or with respect to any Lender or required to be
withheld or deducted from a payment to any Lender, (a) Taxes imposed on or measured by net income (however denominated), franchise Taxes, and branch profits Taxes, in each case, imposed as a result of such Lender being organized under the laws
of, or having its principal office or its applicable lending office located in, the jurisdiction imposing such Tax (or any political subdivision thereof), (b) U.S. federal withholding Taxes imposed on amounts payable to or for the account of
such Lender with respect to an applicable interest in a Loan or Commitment pursuant to a law in effect on the date on which (i) such Lender acquires such interest in the Loan or Commitment (other than pursuant to an assignment request by the
Borrower under Section 1.13) or (ii) such Lender changes its lending office, except in each case to the extent that, pursuant to Section 4.04, amounts with respect to such Taxes were payable either to such Lender’s assignor
immediately before such Lender became a party hereto or to such Lender immediately before it changed its lending office, (c) Taxes attributable to such Lender’s failure to comply with Section 4.04(b) and (d) any U.S. federal
withholding Taxes imposed under FATCA. 
 “Executive Order” shall have the meaning provided in
Section 7.15(a). 
 “OFAC” shall have the meaning provided in Section 7.15(a)(v). 

  
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 “Swap Obligation” means, with respect to any Subsidiary Guarantor, any
obligation to pay or perform under any agreement, contract or transaction that constitutes a “swap” within the meaning of Section 1a(47) of the Commodity Exchange Act. 

“USA PATRIOT Act” means The Uniting and Strengthening America by Providing Appropriate Tools Required to Intercept and
Obstruct Terrorism Act of 2001 (Title III of Pub. L. No. 107-56 (signed into law October 26, 2001)), as amended from time to time. 
 (xxvii) Section 13.01 of the Credit Agreement is hereby amended by (w) inserting the text “(a)” immediately before the first sentence of such Section, (x) adding the parenthetical
“(each, an “Indemnified Person”)” immediately after the text “advisors and agents” appearing in clause (i) thereof, (y) deleting the text “the” immediately after the text “willful misconduct
of” appearing in clause (b) thereof and inserting the text “, or material breach in bad faith of its material obligations under this Agreement or any other Credit Document by, the Indemnified” in lieu thereof, and
(z) inserting the following new subsection (b) at the end of such Section: 
 “(b) To the full extent permitted
by applicable law, the Borrower shall not assert, and hereby waives, any claim against any Indemnified Person, on any theory of liability, for consequential, special, indirect or punitive damages (as opposed to direct or actual damages) arising out
of, in connection with, or as a result of, this Agreement or any agreement or instrument contemplated hereby, the transactions contemplated hereby or thereby, any Loan or the use of the proceeds thereof. No Indemnified Person shall be liable for any
damages arising from the use by unintended recipients of any information or other materials distributed by it through telecommunications, electronic or other information transmission systems in connection with this Agreement or the other Credit
Documents or the transactions contemplated hereby or thereby, except to the extent the liability of such Indemnified Person results from such Indemnified Person’s gross negligence or willful misconduct (as determined by a court of competent
jurisdiction in a final and non-appealable decision).” 
 (xxviii) Section 13.18 of the Credit Agreement is hereby
restated in its entirety as follows: 
 “Section 13.18 USA PATRIOT Act Notice. Each Lender subject to the USA
PATRIOT Act hereby notifies the Borrower that pursuant to the requirements of the USA PATRIOT Act, it is required to obtain, verify and record information that identifies the Borrower and the other Credit Parties and other information that will
allow such Lender to identify the Borrower and the other Credit Parties in accordance with the USA PATRIOT Act and the Borrower agrees to provide such information from time to time to any Lender.” 

(xxix) Schedule IV to the Credit Agreement is hereby restated in its entirety as follows: 

“[Reserved]” 

  
 -11-

 2. Conditions Precedent to Effectiveness. This Second Amendment shall become
effective on the date (the “Second Amendment Effective Date”) when each of the following conditions shall have been satisfied; provided that if the following conditions are not satisfied by April 5, 2013, this Second
Amendment shall not become effective and shall be of no force or effect with respect to the Credit Agreement: 

(i) the Borrower, the Administrative Agent and the Lenders constituting the Required Lenders shall have signed a
counterpart hereof (whether the same or different counterparts) and shall have delivered (including by way of facsimile, pdf or other electronic transmission) the same to the Administrative Agent; 

(ii) all of the representations and warranties made pursuant to Section 3 hereof shall be true and correct in all
material respects on the Second Amendment Effective Date after giving effect to this Second Amendment, with the same effect as though such representations and warranties had been made on and as of the Second Amendment Effective Date (it being
understood and agreed that (x) any representation or warranty which by its terms is made as of a specified date shall be required to be true and correct in all material respects only as of such specified date and (y) any representation or
warranty that is qualified as to “materiality,” “Material Adverse Effect” or similar language shall be true and correct in all respects on such specified date); 

(iii) the Borrower shall have paid any reasonable and documented out-of-pocket expenses of the Administrative Agent
required to be paid or reimbursed pursuant to Section 13.01 of the Credit Agreement, including the reasonable and documented fees, charges and disbursements of counsel for the Administrative Agent; and 

(iv) the Administrative Agent shall have received such other documents, information or agreements regarding the Borrower
as the Administrative Agent shall reasonably request. 
 3. Representations and Warranties. The Borrower represents and
warrants to the Administrative Agent and the Lenders that, as of the date of and after giving effect to this Second Amendment: 

(i) the execution, delivery and performance of this Second Amendment have been duly authorized by all necessary action on the part of the
Borrower; 
 (ii) this Second Amendment is a legal, valid and binding obligation of the Borrower, enforceable against the
Borrower in accordance with its terms, subject to applicable bankruptcy, insolvency, reorganization, moratorium or other similar laws generally affecting creditors’ rights and to general principles of equity; 

(iii) all of the representations and warranties contained in the Credit Agreement and the other Credit Documents are true and correct in
all material respects on the Second Amendment Effective Date after giving effect to this Second Amendment, with the same effect as though such representations and warranties had been made on and as of the Second Amendment Effective Date (it being
understood and agreed that (x) any representation or warranty which by its terms is made as of a specified date shall be required to be true and correct in all material respects only as of such specified date and (y) any representation or
warranty that is qualified as to “materiality,” “Material Adverse Effect” or similar language shall be true and correct in all respects on such specified date); and 

  
 -12-

 (iv) no Default or Event of Default has occurred and is continuing. 

4. General Provisions. 
 (i) Governing Law. THIS SECOND AMENDMENT AND THE RIGHTS AND OBLIGATIONS OF THE PARTIES HEREUNDER SHALL BE CONSTRUED IN ACCORDANCE WITH AND BE GOVERNED BY THE LAW OF THE STATE OF NEW YORK.

 (ii) Execution in Counterparts. This Second Amendment may be executed in any number of counterparts and by the
different parties hereto on separate counterparts, each of which counterparts when executed and delivered shall be an original, but all of which shall together constitute one and the same instrument. Delivery by telecopy or other electronic image
scan transmission of an executed counterpart of a signature page to this Second Amendment shall be effective as delivery of an original executed counterpart of this Second Amendment. The Administrative Agent may also require that any such documents
and signatures delivered by telecopy or other electronic image scan transmission be confirmed by a manually signed original thereof; provided that the failure to request or deliver the same shall not limit the effectiveness of any document or
signature delivered by telecopy or other electronic image scan transmission. A complete set of counterparts shall be lodged with the Borrower and the Administrative Agent. 
 (iii) Severability. Any provision hereof which is held to be invalid, illegal or unenforceable in any jurisdiction shall, as to such jurisdiction, be ineffective to the extent of such invalidity,
illegality or unenforceability without rendering the remaining provisions hereof invalid, illegal or unenforceable in such jurisdiction and without affecting the validity, legality or enforceability of any provision in any other jurisdiction.

 (iv) Successors; Assignment. The terms of this Second Amendment shall be binding upon, and shall inure for the benefit
of, the parties hereto and their respective successors and assigns; provided that the Borrower may not assign or transfer any of its rights, obligations or interest hereunder without the prior written consent of each Lender. 

(v) Effect on Credit Documents. (i) Except as expressly set forth herein, this Second Amendment shall not by implication or
otherwise limit, impair, constitute a waiver of or otherwise affect the rights and remedies of the Lenders or the Agents under the Credit Agreement or any other Credit Document, and shall not alter, modify, amend or in any way affect any of the
terms, conditions, obligations, covenants or agreements contained in the Credit Agreement or any other provision of the Credit Agreement or of any other Credit Document, all of which are ratified and affirmed in all respects and shall continue in
full force and effect. Nothing herein shall be deemed to entitle the Borrower to receive consent to, or a waiver, amendment, modification or other change of, any of the terms, conditions, obligations, covenants or agreements contained in the Credit
Agreement or any other Credit Document in similar or different circumstances. 

  
 -13-

 (vi) Reference to Amendment. On and after the Second Amendment Effective Date, each
reference in the Credit Agreement to “this Agreement”, “hereunder”, “hereof”, “herein”, or words of like import, and each reference to the Credit Agreement in any other Credit Document shall be deemed a
reference to the Credit Agreement as modified hereby. This Second Amendment shall constitute a “Credit Document” for all purposes of the Credit Agreement and the other Credit Documents. 

* * * 

  
 -14-

 IN WITNESS WHEREOF, the parties hereto have caused this Second Amendment to the Credit
Agreement to be executed by their respective officers thereunto duly authorized, as of the date first set forth above. 
  

			
	FLOWERS FOODS, INC.
		
	By:	 	/s/ R. Steve Kinsey
		 	Name: R. Steve Kinsey
		 	Title: EVP & CFO

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 DEUTSCHE BANK AG NEW YORK BRANCH,
 individually as Administrative Agent and as a
 Lender

		
	By:	 	/s/ Heidi Sandquist
		 	 Name: Heidi Sandquist

Title: Director

		
	By:	 	/s/ Ming K. Chu
		 	 Name: Ming K. Chu
 Title:
Vice President

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 BANK OF AMERICA, N.A.

	
	 
		
	By:	 	/s/ David Catherall
		 	 Name: David Catherall

Title: Managing Director

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 Branch Banking and Trust Company

		
	By:	 	/s/ B. Echols
		 	 Brantley Echols
 Senior Vice
President

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 COOPERATIEVE CENTRALE RAIFFEISEN- BOETENLEENBANK B.A. “RABOBANK NEDERLAND”, NEW YORK BRANCH

	
	 
		
	By:	 	/s/ Theodore W. Cox
		 	 Name: Theodore W. Cox

Title: Executive Director

		
	By:	 	/s/ Stewart Kalish
		 	 Name: Stewart Kalish
 Title:
Executive Director

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 REGIONS BANK

		
	By:	 	/s/ J. Ryan Hammack
		 	 Name: J. Ryan Hammack

Title: Assistant Vice President

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 The Northern Trust Company

	
	 
		
	By:	 	/s/ Kathryn S. Reuther
		 	 Name: Kathryn Schad Reuther

Title: SVP

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 PNC Bank, National Association

		
	By:	 	/s/ Susan J. Dimmick
		 	 Name: Susan J. Dimmick

Title: Senior Vice President

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 ROYAL BANK OF CANADA

		
	By:	 	/s/ G. MacArthur
		 	 Name: Gordon MacArthur

Title: Authorized Signatory

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 WELLS FARGO BANK, NATIONAL ASSOCIATION

		
	By:	 	/s/ Ron Edwards
		 	 Name: Ron Edwards
 Title:
Senior Vice President

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 AgFirst Farm Credit Bank

		
	By:	 	/s/ Bruce B. Fortner
		 	 Bruce B Fortner
 Vice
President

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 CoBank, ACB

	
	 
		
	By:	 	/s/ M Tousignant
		 	 Name: Michael Tousignant

Title: Vice President

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 NAME OF INSTITUTION 
  

Farm Credit Services of America, PCA

		
	By:	 	/s/ Curt A. Brown
		 	 Name: Curt A. Brown
 Title:
Vice President

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 GreenStone Farm Credit Services, ACA/FLCA

		
	By:	 	/s/ Alfred S. Compton, Jr.
		 	 Name: Alfred S. Compton, Jr.

Title: SVP/Managing Director

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement] 

 
			
	 SIGNATURE PAGE TO THE SECOND AMENDMENT, DATED AS OF THE DATE FIRST ABOVE WRITTEN, TO THE CREDIT AGREEMENT, DATED AS OF
OCTOBER 24, 2003, AS AMENDED AND RESTATED AS OF OCTOBER 29, 2004, AS FURTHER AMENDED AND RESTATED AS OF JUNE 6, 2006, AS FURTHER AMENDED AND RESTATED AS OF MAY 20, 2011, AND AS AMENDED AS OF NOVEMBER 16, 2012, AMONG FLOWERS
FOODS, INC., THE VARIOUS LENDERS PARTY THERETO AND DEUTSCHE BANK AG NEW YORK BRANCH, AS ADMINISTRATIVE AGENT
  
 NAME OF INSTITUTION 
  

SunTrust Bank

		
	By:	 	/s/ Peter L. Johnson
		 	 Name: Peter Johnson
 Title:
Vice President

  
 [Signature
Page to Second Amendment to Flowers A&R Credit Agreement]EX-10.1

 Exhibit 10.1 
 2013 Conceptus Executive Bonus Plan 
  

 

Plan:         FY13 EBP – Executive Bonus Plan 

 

	I.	Objective 

 Conceptus’ Executive Bonus Plan (hereinafter referred to as “EBP”) is intended to recognize and reward executive officers of the Company who are subject to
Section 16 of the Securities Exchange Act of 1934, as amended (collectively, the “Executives”), including the Chief Executive Officer (“CEO”) and Named Executive Officers (“NEOs”), who achieve goals that support,
and are aligned with, the Company’s strategic goals. The purpose of the plan is to: 
  

	 	•	 	 Focus Executive efforts on goals of critical importance to the Company’s and each department’s business plan. 

 

	 	•	 	 Strengthen the ability of the Company to attract and retain high caliber, critical personnel. 

 

	 	•	 	 Provide bonus opportunities that reward above average performance. 

 

	II.	Determination of the Fund 

 To determine the actual dollars in the Plan, each Executive has a defined target incentive opportunity, expressed as a percent of base salary, which is recommended for approval each year by the CEO (other
than with respect to the CEO’s own opportunity) and approved by the Compensation Committee and the Board of Directors. This target is used to determine the amount of funding contributed to the overall award pool for each Executive. 

 

	III.	Effective Date 

The effective date of this program is 1 January 2013, the beginning of the plan year, and will continue in effect until
31 December 2013, or until terminated or amended by the Compensation Committee and the Board of Directors. This plan supersedes all prior Executive incentive cash compensation plans. 

 

	IV.	Eligibility 

 The
participants must meet the following criteria to be eligible to participate in the Incentive Plan: 
  

	 	•	 	 Regular, full-time employee status; 

  

	 	•	 	 Hired on or before September 30th of the current fiscal year; 

 

	 	•	 	 A participant must not be a participant in any other variable pay plan at Conceptus including any sales Commission Plan; 

	 	•	 	 A participant must be employed by Conceptus as a regular full-time, Executive on the day the bonus is paid to be eligible to receive any Incentive Plan
award and not on a performance improvement plan at the end of the year. 

  

	 	•	 	 The approved Target Bonus for each Executive is a percentage of the Executive’s base salary at the close of the fiscal year, and for the current
EBP are as follows: 

  

			
	 EXECUTIVE
PARTICIPANT
CATEGORY
	  	TARGET
AWARD: % of
BASE SALARY
	 CEO
	  	100%
	 EVP, CFO
	  	60%
	 EVP, Chief Commercial Officer
	  	60%
	 EVP, General Counsel
	  	60%
	 EVP, R&D
	  	50%
	 EVP, Operations
	  	50%
	 EVP, Human Resources
	  	50%
	 VP, Clinical & Regulatory Affairs
	  	40%

 Incentive Objectives 
 There are three components to achievement of an award: 20% personal MBO, 48% sales plan and 32% aEBITDA plan (based on a 60/40 split between Sales and aEBITDA). The sales plan and aEBITDA plan shall be
established by the Compensation Committee and Board of Directors and set forth in the minutes of the applicable meeting. Achievement payout is straight forward for personal MBO’s. The final determination of the Executive’s achievement of
personal MBO’s will be made by the Compensation Committee and the Board of Directors after receiving the CEO’s recommendation for personal MBO achievement for all Executives other than the CEO. For sales and aEBITDA, payouts will be based
on the following company performance levels: 
  

													
	 Sales Plan
 Achievement
	  	Payout	 	 	aEBITDA Plan
Achievement*	 	 	Payout	 
	 <95%
	  	 	0	% 	 	 	<95	% 	 	 	0	% 
	 95%
	  	 	50	% 	 	 	95	% 	 	 	50	% 
	 96%
	  	 	60	% 	 	 	96	% 	 	 	60	% 
	 97%
	  	 	70	% 	 	 	97	% 	 	 	70	% 
	 98%
	  	 	80	% 	 	 	98	% 	 	 	80	% 
	 99%
	  	 	90	% 	 	 	99	% 	 	 	90	% 
	 100%
	  	 	100	% 	 	 	100	% 	 	 	100	% 

  

	*	aEBITDA achievement is calculated after bonus accrual 

 aEBITDA is defined as operating income plus stock compensation, depreciation and amortization. 

 In order for any payout to occur for any of the three EBP components, there is a threshold
requiring both Sales Plan achievement and an aEBITDA Plan achievement to be at 95% minimum. There will be overachievement permitted based exclusively on Sales Plan Achievement as follows: 

 

					
	 2013

Sales Plan
 Achievement
	  	2013
Payout	 
	 101%
	  	 	106	% 
	 102%
	  	 	112	% 
	 103%
	  	 	118	% 
	 104%
	  	 	124	% 
	 105%
	  	 	130	% 
	 106%
	  	 	136	% 
	 107%
	  	 	143	% 
	 108%
	  	 	150	% 

 The actual payout percentage will be interpolated between the points in the above table, based on the
actual Sales Plan achievement percentage. For example, Sales Plan achievement of 101.5% would result in an earned payout of 109%. 
 The payout percentage applies to the individual’s entire bonus payment, not just the Sales component. 
  

	VI.	Bonus Opportunity & Award 

 The target award opportunity will be expressed as a percentage of the participant’s base salary at the close of the fiscal year. The award for Executives other than the CEO will be recommended by the
CEO and approved by the Compensation Committee and Board of Directors and will be consistent with the participant’s peers within the company. The award for the CEO will be approved by the Compensation Committee and Board of Directors.

 The amount that a participant actually receives for the full fiscal year will be based upon the extent to which the set
objectives have been achieved. The participant will receive a percentage of the total award opportunity corresponding to the percentage of each objective accomplished and the weight assigned to the objective. Evaluations of performance against
individual and financial objectives are made for the full year prior to fiscal year-end payment. 

	VII.	Performance Goal and Payout 

 MBO’s are established at the start of the year for each Executive to ensure individual priorities are aligned with the Company’s corporate goals. These individual objects or MBO’s reflect
the key priorities and results that the Plan participant as an individual will be accountable for under the Plan. Performance against the MBO’s of the Executives other than the CEO will be assessed by the CEO and approved by the Compensation
Committee and Board of Directors at the end of the year and will impact the final incentive award (if any) a Plan participant earns under the Plan. Performance against the MBO’s for the CEO will be assessed and approved by the Compensation
Committee and Board of Directors. 
 Bonus awards for each participant will be calculated by the Finance Department. The awards
will be made as soon as practical after the completion of the audit and issuance of year-end earnings press release. Generally, the awards will be distributed within three months after the end of the fiscal year and, in any event, prior to the last
day of the second quarter during which the determination is made. 
  

	VIII.	Plan Administration 

Pro-rated Awards. Individuals who are promoted to eligible positions during the plan year, new hires into eligible positions and
eligible participants who are either on leave or on active written warning for part of the year may be awarded partial bonuses under this program, based on the accomplished objectives and their respective weights, subject to recommendation of the
CEO and the approval of the Compensation Committee and Board of Directors. 
 Transfers. In the event of transfer of an
eligible participant to another position or department in which the participant no longer qualifies as an Executive, the CEO will evaluate EBP results for a prorated award (see Prorated Awards above) at the end of the year, and forward copies to the
Human Resources Department. The CEO will be responsible for setting the key business plan objectives for the balance of the year, if applicable, and forwarding the original to Human Resources. Awards based on these objectives will be pro-rated (see
Pro-rated Awards above) as well, for end of the year payment. 
 Authority. The Compensation Committee shall have the full
power and authority to construe, interpret and administer the plan. All decisions, actions or interpretations of the Compensation Committee and the Board of Directors shall be final and conclusive and binding on all parties. This program shall be
administered by the Human Resources Department. 
  

	IX.	General Provisions 

The sales plan and the aEBITDA plan for 2013 may be reviewed and revised at the discretion of the Compensation Committee and Board of
Directors. 
 Nothing in this plan shall be construed to limit in any way the right of Conceptus, Inc. to terminate an
employee’s employment at any time, with or without cause or notice, nor shall it be evidence of any agreement or understanding, expressed or implied, that Conceptus or any of its subsidiaries will employ an employee in any particular position,
for any particular period of time, ensure participation in any incentive programs, or the granting of awards from such programs as they may from time to time exist or be constituted. Conceptus reserves the right to discontinue or alter the plan at
its sole discretion at any time with or without notice. 

 ACKNOWLEDGEMENT 
 I,
                                        , hereby
acknowledge that I have received, read and understand the 2013 Conceptus Executive Bonus Plan and agree to the conditions therein. 
  

					
	  
	 		 	  

	Signature	 		 	Date

  
 A-1

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