SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13G

Under the Securities Exchange Act of 1934

GREEN PLAINS PARTNERS LP

(Name of Issuer)

COMMON STOCK

(Title of Class of Securities)

393221106

(CUSIP Number)

June 26, 2015

(Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

¨ Rule 13d-1(b)

x Rule 13d-1(c)

¨ Rule 13d-1(d)

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

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         Green Plains Partners LP (the “Company”)

         450 Regency Parkway

         Suite 400

         Omaha, NE 68114

         United States

(1) Atlas Master Fund, Ltd. is a Cayman corporation (“AMF”), with its principal business office at c/o Maples Corporate Services Limited, P.O. Box 309, Ugland House, George Town, Grand Cayman KY1-1104, Cayman Islands, British West Indies.

(2) Atlas Global, LLC is a Delaware limited liability company (“AG”), with its principal business office at 181 West Madison, Suite 3600, Chicago, IL 60602. AG owns 13.47% of the equity interests in AMF.

(3) Atlas Global Investments, Ltd. is a Cayman corporation (“AGI”), with its principal business office at c/o Maples Corporate Services Limited, P.O. Box 309, Ugland House, George Town, Grand Cayman KY1-1104, Cayman Islands, British West Indies. AGI owns 20.56% of the equity interests in AMF.

(4) Atlas Institutional Fund, LLC is a Delaware limited liability company (“AIF LLC”), with its principal business office at 181 West Madison, Suite 3600, Chicago, IL 60602. AIF LLC owns 5.10% of the equity interests in AMF.

(5) Atlas Institutional Fund, Ltd. is a Cayman corporation (“AIF LTD”), with its principal business office at c/o Maples Corporate Services Limited, P.O. Box 309, Ugland House, George Town, Grand Cayman KY1-1104, Cayman Islands, British West Indies. AIF LTD owns 15.38% of the equity interests in AMF.

(6) Atlas Institutional Fund II, LLC is a Delaware limited liability company (“AIF2 LLC”), with its principal business office at 181 West Madison, Suite 3600, and Chicago, IL 60602. AIF2 LLC owns 9.83% of the equity interests in AMF.

(7) Atlas Institutional Fund II, Ltd. is a Cayman corporation (“AIF2 LTD”), with its principal business office at c/o Maples Corporate Services Limited, P.O. Box 309, Ugland House, George Town, Grand Cayman KY1-1104, Cayman Islands, British West Indies. AIF2 LTD owns 24.83% of the equity interests in AMF.

Page 16 of 30 Pages

(8) Atlas Global Japan Unit Trust is a Cayman exempted unit trust (“AGJ”), with its principal business office at c/o CIBC Bank and Trust Company (Cayman) Limited, CIBC Financial Centre, 11 Dr. Roy’s Drive-3^rd Floor, P.O. Box 694, Grand Cayman, Cayman Islands, British West Indies. AGJ owns 6.22% of the equity interests in AMF.

(9) Atlas Enhanced Master Fund, Ltd. is a Cayman corporation (“AEMF”), with its principal business office at c/o Maples Corporate Services Limited, P.O. Box 309, Ugland House, George Town, Grand Cayman KY1-1104, Cayman Islands, British West Indies.

(10) Atlas Enhanced Fund, L.P. is a Delaware limited partnership (“AEF LP”), with its principal business office at 181 West Madison, Suite 3600, Chicago, IL 60602. AEF LP owns 26.38% of the equity interests in AEMF.

(11) Atlas Enhanced Fund, Ltd. is a Cayman corporation (“AEF LTD”), with its principal business office at c/o Maples Corporate Services Limited, P.O. Box 309, Ugland House, George Town, Grand Cayman KY1-1104, Cayman Islands, British West Indies. AEF LTD owns 73.60% of the equity interests in AEMF.

(12) Lyxor/Balyasny Atlas Enhanced Fund Limited is a Jersey limited corporation (“LYXOR”), with its registered office at 18 Esplanade, St. Helier, Jersey JE4 8RT, Channel Islands.

(13) Balyasny Asset Management L.P. is a Delaware limited partnership (“BAM”), with its principal business office at 181 West Madison, Suite 3600, and Chicago, IL 60602. BAM is the investment manager to each of AMF, AG, AGI, AIF LLC, AIF LTD, AIF2 LLC, AIF2 LTD, AGJ, AEMF, AEF LP, AEF LTD, and LYXOR.

(14) Dmitry Balyasny, a United States citizen whose business address is 181 West Madison, Suite 3600, Chicago, IL 60602. Dmitry Balyasny is the sole managing member of the general partner of BAM.

         Common Stock

Page 17 of 30 Pages

Not Applicable

AMF

(a)    Amount Beneficially Owned:

   392,587

(b)    Percent of Class:

   2.47%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   392,587

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   392,587

        (iv)    Shared power to dispose or to direct disposition of:

   None

        AG

(a)    Amount Beneficially Owned:

By virtue of its ownership of 13.47% of the equity interest in AMF, AG may be deemed to beneficially own the 392,587 Shares of the Company’s Common Stock beneficially owned by AMF.

Page 18 of 30 Pages

(b)    Percent of Class:

   2.47%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   392,587

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   392,587

        (iv)    Shared power to dispose or to direct disposition of:

   None

AGI

(a)    Amount Beneficially Owned:

By virtue of its ownership of 20.56% of the equity interest in AMF, AGI may be deemed to beneficially own the 392,587 Shares of the Company’s Common Stock beneficially owned by AMF.

(b)    Percent of Class:

   2.47%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   392,587

        (ii)     Shared power to vote or to direct vote:

   None

Page 19 of 30 Pages

        (ii)     Sole power to dispose or direct disposition of:

   392,587

        (iv)    Shared power to dispose or to direct disposition of:

   None

AIF LLC

(a)    Amount Beneficially Owned:

By virtue of its ownership of 5.10% of the equity interest in AMF, AIF LLC may be deemed to beneficially own the 392,587 Shares of the Company’s Common Stock beneficially owned by AMF.

(b)    Percent of Class:

   2.47%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   392,587

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   392,587

        (iv)    Shared power to dispose or to direct disposition of:

   None

Page 20 of 30 Pages

AIF LTD

(a)    Amount Beneficially Owned:

By virtue of its ownership of 15.38% of the equity interest in AMF, AIF LTD may be deemed to beneficially own the 392,587 Shares of the Company’s Common Stock beneficially owned by AMF.

(b)    Percent of Class:

   2.47%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   392,587

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   392,587

        (iv)    Shared power to dispose or to direct disposition of:

   None

AIF2 LLC

(a)    Amount Beneficially Owned:

By virtue of its ownership of 9.83% of the equity interest in AMF, AIF2 LLC may be deemed to beneficially own the 392,587 Shares of the Company’s Common Stock beneficially owned by AMF.

(b)    Percent of Class:

   2.47%

Page 21 of 30 Pages

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   392,587

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   392,587

        (iv)    Shared power to dispose or to direct disposition of:

   None

AIF2 LTD

(a)    Amount Beneficially Owned:

By virtue of its ownership of 24.83% of the equity interest in AMF, AIF2 LTD may be deemed to beneficially own the 392,587 Shares of the Company’s Common Stock beneficially owned by AMF.

(b)    Percent of Class:

   2.47%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   392,587

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   392,587

Page 22 of 30 Pages

        (iv)    Shared power to dispose or to direct disposition of:

   None

AGJ

(a)    Amount Beneficially Owned:

By virtue of its ownership of 6.22% of the equity interest in AMF, AGJ may be deemed to beneficially own the 392,587 Shares of the Company’s Common Stock beneficially owned by AMF.

(b)    Percent of Class:

   2.47%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   392,587

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   392,587

        (iv)    Shared power to dispose or to direct disposition of:

   None

AEMF

(a)    Amount Beneficially Owned:

   567,743

(b)    Percent of Class:

   3.57%

Page 23 of 30 Pages

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   567,743

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   567,743

        (iv)    Shared power to dispose or to direct disposition of:

   None

AEF LP

(a)    Amount Beneficially Owned:

By virtue of its ownership of 26.38% of the equity interest in AEMF, AEF LP may be deemed to beneficially own the 567,743 Shares of the Company’s Common Stock beneficially owned by AEMF.

(b)    Percent of Class:

   3.57%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   567,743

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   567,743

Page 24 of 30 Pages

        (iv)    Shared power to dispose or to direct disposition of:

   None

AEF LTD

(a)    Amount Beneficially Owned:

By virtue of its ownership of 73.60% of the equity interest in AEMF, AEF LTD may be deemed to beneficially own the 567,743 Shares of the Company’s Common Stock beneficially owned by AEMF.

(b)    Percent of Class:

   3.57%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   567,743

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   567,743

        (iv)    Shared power to dispose or to direct disposition of:

   None

LYXOR

(a)    Amount Beneficially Owned:

39,670

(b)    Percent of Class:

0.25%

Page 25 of 30 Pages

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   39,670

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   39,670

        (iv)    Shared power to dispose or to direct disposition of:

   None

BAM

(a)    Amount Beneficially Owned:

By virtue of its position as investment manager to each of AMF, AG, AGI, AIF LLC, AIF LTD, AIF2 LLC, AIF2 LTD, AGJ, AEMF, AEF LP, AEF LTD, and LYXOR, BAM may be deemed to beneficially own the 1,000,000 Shares of the Company’s Common Stock beneficially owned by AMF, AG, AGI, AIF LLC, AIF LTD, AIF2 LLC, AIF2 LTD, AGJ, AEMF, AEF LP, AEF LTD, and LYXOR.

(b)    Percent of Class:

   6.29%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   1,000,000

        (ii)     Shared power to vote or to direct vote:

   None

Page 26 of 30 Pages

        (iii)    Sole power to dispose or direct disposition of:

   1,000,000

        (iv)    Shared power to dispose or to direct disposition of:

   None

Dmitry Balyasny

(a)    Amount Beneficially Owned:

By virtue of his position as the sole managing member of the general partner of BAM, Mr. Balyasny may be deemed to beneficially own the 1,000,000 Shares of the Company’s Common Stock beneficially owned by BAM.

(b)    Percent of Class:

   6.29%

(c)    Number of Shares as to which person has:

        (i)      Sole power to vote or to direct vote:

   1,000,000

        (ii)     Shared power to vote or to direct vote:

   None

        (iii)    Sole power to dispose or direct disposition of:

   1,000,000

        (iv)    Shared power to dispose or to direct disposition of:

   None

        Applicable

Page 27 of 30 Pages

Not Applicable

Not Applicable

Not Applicable

Not Applicable

By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.

Page 28 of 30 Pages

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Date: July 7, 2015

Page 29 of 30 Pages

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