GPP Green Plains Partners LP

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

Amendment No. 2

to

SCHEDULE 13E-3

TRANSACTION STATEMENT UNDER SECTION 13(e) OF THE

SECURITIES EXCHANGE ACT OF 1934 AND

RULE 13e-3 THEREUNDER

Rule 13e-3 Transaction Statement Under Section 13(e)

of the Securities Exchange Act of 1934

GREEN PLAINS PARTNERS LP

(Name of Issuer)

Green Plains Partners LP

Green Plains Inc.

Green Plains Holdings LLC

GPLP Holdings Inc.

GPLP Merger Sub LLC

(Names of Persons Filing Statement)

Common Units Representing Limited Partner Interests

(Title of Class of Securities)

393221106

(CUSIP Number of Class of Securities)

This statement is filed in connection with (check the appropriate box):

Check the following box if the soliciting materials or information statement referred to in checking box (a) are preliminary copies:  ☐

Check the following box if the filing is a final amendment reporting the results of the transaction:  ☐

Neither the SEC nor any state securities regulatory agency has approved or disapproved the Merger, passed upon the merits or fairness of the Merger or passed upon the adequacy or accuracy of the disclosure in this document. Any representation to the contrary is a criminal offense.

INTRODUCTION

This Amendment No. 2 to the Rule 13e-3 Transaction Statement on Schedule 13E-3 (this “Amendment No. 2”) amends and supersedes the Rule 13E-3 Transaction Statement on Schedule 13E-3 originally filed on October 17, 2023 (together with the exhibits filed thereto, the “Original Statement”), as amended by Amendment No. 1 thereto filed on November 17, 2023 (together with the exhibits filed thereto, “Amendment No. 1” and the Original Statement as amended by Amendment No. 1 and this Amendment No. 2, together with the exhibits filed hereto and thereto, this “Amended Transaction Statement”) and is being filed with the Securities and Exchange Commission (the “SEC”) pursuant to Section 13(e) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), by: (i) Green Plains Partners LP, a Delaware limited partnership (“GPP”) and the issuer of the common units representing limited partner interests in GPP (“GPP Common Units,” and the holders of GPP Common Units, the “GPP Unitholders”) that are subject to the Rule 13e-3 transaction, (ii) Green Plains Inc., an Iowa corporation (“GPRE”), (iii) GPLP Holdings Inc., a Delaware corporation and a wholly owned subsidiary of GPRE (“Holdings”), (iv) GPLP Merger Sub LLC, a Delaware limited liability company and a wholly owned subsidiary of Holdings (“Merger Sub”), and (v) Green Plains Holdings LLC, a Delaware limited liability company and the general partner of GPP (the “General Partner”). Collectively, the persons filing this Amended Transaction Statement are referred to as the “filing persons.”

This Amended Transaction Statement relates to the Agreement and Plan of Merger, dated as of September 16, 2023 (as the same may be amended or supplemented from time to time, the “Merger Agreement”), by and among GPRE, Holdings, Merger Sub, GPP and the General Partner, pursuant to which Merger Sub will merge with and into GPP, with GPP surviving as an indirect, wholly owned subsidiary of GPRE (the “Merger”).

Under the terms of the Merger Agreement, at the effective time of the Merger (the “Effective Time”), each outstanding GPP Common Unit other than GPP Common Units owned by GPRE, the General Partner and their respective affiliates (each, a “GPP Public Common Unit” and the holders of such units, the “GPP Unaffiliated Unitholders”) will be converted into the right to receive, subject to adjustment as described in the Merger Agreement, (i) 0.405 shares of common stock, par value $0.001 per share, of GPRE (the “GPRE Common Stock” and the shares of GPRE Common Stock to be issued in the Merger, the “Stock Consideration”) and (ii) an amount of cash equal to the sum of (a) $2.00 plus (b) the product of (x) $0.455 divided by 90, multiplied by (y) the number of days from, but excluding, the last day of the calendar quarter with respect to which the General Partner has declared a quarterly cash distribution to the holders of GPP Common Units of no less than $0.455 per GPP Common Unit with a record date prior to the date of the closing of the Merger (the “Closing Date”), to, but excluding, the Closing Date, computed on the basis of a 360-day year comprised of twelve 30-day months and the actual number of days for any period less than a calendar month, and rounded to the nearest whole cent, without interest (the “Cash Consideration” and, together with the Stock Consideration, the “Merger Consideration”). In addition, at the Effective Time, each of the outstanding awards relating to a GPP Common Unit issued under a Partnership Long-Term Incentive Plan (as defined in the Merger Agreement) will become fully vested and will be automatically canceled and converted into the right to receive, with respect to each GPP Common Unit subject thereto, the Merger Consideration (plus any accrued but unpaid amounts in relation to distribution equivalent rights). Except for the incentive distribution rights representing limited partner interests in GPP, which will be automatically canceled immediately prior to the Effective Time for no consideration in accordance with the First Amended and Restated Agreement of Limited Partnership of GPP, dated as of July 1, 2015 (as amended, the “Partnership Agreement”), the limited partner interests in GPP owned by GPRE, the General Partner and their respective affiliates prior to the Effective Time will remain outstanding as limited partner interests in the surviving entity. The economic general partner interest in GPP will remain outstanding as a general partner interest in the surviving entity immediately following the Effective Time, and the General Partner will continue as the sole general partner of the surviving entity. No fractional shares of GPRE Common Stock will be issued in the Merger; instead, all fractional shares of GPRE Common Stock to which a GPP Unaffiliated Unitholder otherwise would have been entitled will be aggregated and the resulting fraction will be rounded up to the nearest whole share of GPRE Common Stock.

The closing of the Merger will take place on the second business day after the satisfaction or waiver of the conditions set forth in the Merger Agreement (other than conditions that by their nature are to be satisfied at the Closing, but subject to the satisfaction or waiver of those conditions), or at such other place and at such later date and time as GPRE and GPP may agree. The Merger will become effective at such time as the certificate of merger effecting the Merger (the “Certificate of Merger”) has been duly filed with the Secretary of State of the State of Delaware or at such later date or time as may be agreed by GPRE and GPP in writing and specified in the Certificate of Merger. On September 15, 2023, the board of directors of GPRE (the “GPRE Board”), by unanimous vote (i) determined that the Merger Agreement and the transactions contemplated thereby, including the Merger and the issuance of GPRE Common Stock as part of the Merger Consideration (the “GPRE Stock Issuance”), are in the best interests of GPRE and its shareholders and (ii) approved and authorized the execution and delivery of the Merger

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Agreement and that certain Support Agreement, dated as of September 16, 2023, by and among GPP, GPRE, Jerry L. Peters, the Jerry L. Peters and Kari A. Peters Joint Trust Agreement, dated October 21, 2020, Michelle S. Mapes, Todd A. Becker and G. Patrich Simpkins Jr. (such holders and GPRE, collectively, the “Support Parties”) (the “Support Agreement” and, together with the Merger Agreement, the “Transaction Documents”) and the consummation of the transactions contemplated thereby, including the Merger and the GPRE Stock Issuance, on the terms and subject to the conditions set forth in the Transaction Documents.

On September 16, 2023, the conflicts committee (the “Conflicts Committee”) of the board of directors of the General Partner (the “GP Board”), by unanimous vote, in good faith, (i) determined that the Merger Agreement and the transactions contemplated thereby, including the Merger, are in the best interests of GPP, including the GPP Unaffiliated Unitholders, (ii) approved the Transaction Documents and the transactions contemplated thereby, including the Merger, on the terms and subject to the conditions set forth in the Transaction Documents (the foregoing constituting “Special Approval” as defined in the Partnership Agreement) and (iii) recommended to the GP Board the approval by the GP Board of the Transaction Documents and the execution, delivery and performance of the Transaction Documents and the transactions contemplated thereby, including the Merger.

On September 16, 2023, following receipt of the recommendation of the Conflicts Committee, the GP Board (acting, in part, based upon the recommendation of the Conflicts Committee), by unanimous vote, in good faith, (i) determined that the Merger Agreement and the transactions contemplated thereby, including the Merger, are in the best interests of GPP, including the GPP Unaffiliated Unitholders, (ii) approved the Transaction Documents and the transactions contemplated thereby, including the Merger, (iii) authorized the execution and delivery of the Transaction Documents and the consummation of the transactions contemplated thereby, including the Merger, on the terms and subject to the conditions set forth in the Transaction Documents and (iv) directed that the Merger Agreement and the Merger be submitted to a vote of the limited partners of GPP (the “GPP Limited Partners”) for approval pursuant to Section 14.3 of the Partnership Agreement and authorized the GPP Limited Partners to act by written consent pursuant to Section 13.11 of the Partnership Agreement.

Pursuant to the Partnership Agreement, the approval of the Merger Agreement and the Merger by GPP requires the affirmative vote or written consent of the holders of a majority of the outstanding GPP Common Units (the “Required Limited Partner Written Consent”). Under the Support Agreement, each Support Party has irrevocably and unconditionally agreed to deliver a written consent, covering all of the GPP Common Units beneficially owned by such Support Party, approving the Merger Agreement and the transactions contemplated thereby, including the Merger, and any other matters necessary for the consummation of the transactions contemplated by the Merger Agreement (the “Written Consent”), as promptly as practicable after the effectiveness of the Consent Solicitation Statement/Prospectus (as defined below). As of September 16, 2023, the date of the Merger Agreement, and November 30, 2023, GPRE beneficially owned 11,586,548 GPP Common Units, Jerry L. Peters beneficially owned 6,183 GPP Common Units, the Jerry L. Peters and Kari A. Peters Joint Trust Agreement, dated October 21, 2020, beneficially owned 46,600 GPP Common Units, Michelle S. Mapes beneficially owned 14,242 GPP Common Units, Todd A. Becker beneficially owned 2,856 GPP Common Units and G. Patrich Simpkins Jr. beneficially owned 5,000 GPP Common Units. Collectively, the Support Parties beneficially owned 11,661,429 GPP Common Units as of September 16, 2023, the date of the Merger Agreement, and November 30, 2023, representing approximately 50.1% of the outstanding GPP Common Units. Accordingly, the delivery of the Written Consent will be sufficient to approve the Merger Agreement and the transactions contemplated thereby, including the Merger, on behalf of the GPP Limited Partners.

On November 17, 2023, GPRE filed with the SEC an amended registration statement on Form S-4, which included a notice of solicitation of written consent and a consent solicitation statement/prospectus with respect to (i) the issuance of shares of GPRE Common Stock required to fund the Stock Consideration and (ii) the solicitation of written consents from the GPP Limited Partners. The registration statement on Form S-4 became effective under the Securities Act of 1933, as amended (the “Securities Act”) on December 1, 2023. Concurrently with the filing of this Amended Transaction Statement and in connection with the Merger Agreement and the transactions contemplated thereby, including the Merger and the solicitation of written consents from the GPP Limited Partners, (i) GPRE is filing with the SEC a prospectus pursuant to Rule 424(b)(3) promulgated under the Securities Act (the “GPRE Prospectus”), and (ii) GPP is filing with the SEC a definitive consent solicitation statement on Form DEFM14A pursuant to Section 14(a) of the Exchange Act (the “GPP Consent Solicitation Statement”). Each of the GPRE Prospectus and the GPP Consent Solicitation Statement included a notice of solicitation of written consent and a consent solicitation statement/prospectus (the “Consent Solicitation Statement/Prospectus”). GPP expects to first mail the Consent Solicitation Statement/Prospectus to GPP Limited Partners on or about December 6, 2023. A copy of the Consent Solicitation Statement/Prospectus is attached hereto as Exhibit (a)(1). A copy of the Merger Agreement is attached as Annex A to the Consent Solicitation Statement/Prospectus. A copy of the Support Agreement is attached as Annex B to the Consent Solicitation Statement/Prospectus. All references in this Amended Transaction Statement to Items numbered 1001 to 1016 are references to Items contained in Regulation M-A under the Exchange Act.

Pursuant to General Instruction F to Schedule 13E-3, the information contained in the Consent Solicitation Statement/Prospectus, including all annexes thereto, is incorporated herein by reference in its entirety and responses to each item herein are qualified in their entirety by the information contained in the Consent Solicitation Statement/Prospectus and the annexes thereto. The cross-references below are being supplied pursuant to General Instruction G to Schedule 13E-3 and show the location in the Consent Solicitation Statement/Prospectus of the information required to be included in response to the items of Schedule 13E-3. Terms used but not defined in this Amended Transaction Statement have the meanings given to them in the Consent Solicitation Statement/Prospectus.

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All information concerning GPP contained in, or incorporated by reference into, this Amended Transaction Statement was supplied by GPP. Similarly, all information concerning any other filing person contained in, or incorporated by reference into, this Amended Transaction Statement was supplied by such filing person.

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SIGNATURES

After due inquiry and to the best of each of the undersigned’s knowledge and belief, each of the undersigned certifies that the information set forth in this statement is true, complete and correct.

Dated as of December 4, 2023

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