Second Amendment to Investor Rights Agreement

Exhibit 4.5

Second Amendment to Investor Rights Agreement

     This Second Amendment (the “ Amendment ”) is entered into as of August 28, 2009, by and among Advanced BioEnergy, LLC, a Delaware limited liability company (the “ Company ”), and South Dakota Wheat Growers Association, a South Dakota cooperative (“ SDWG ”).

Background

     A. On November 8, 2006, the Company and SDWG entered into an investor rights agreement (as amended, the “ SDWG Investor Rights Agreement ”) in connection with the purchase by the Company of SDWG’s limited partnership interest in Heartland Grain Fuels, L.P. (“ HGF ”).

     B. On August 21, 2009, the Company entered into a subscription agreement with Hawkeye Energy Holdings, LLC (“ Hawkeye ”) pursuant to which the Company agreed to enter into a registration rights agreement with Hawkeye (the “ Hawkeye Registration Rights Agreement ”), provided the Company first obtained, among other third party consents, SDWG’s consent to grant such rights.

     C. In connection with the execution of the Hawkeye Registration Rights Agreement, ABE and SDWG desire to amend the SDWG Investor Rights Agreement as follows:

Agreement

      1.  Amendment to Article 1. Article 1 of the SDWG Investor Rights Agreement is hereby amended and restated in its entirety as set forth in the attached Exhibit A .

      2.  Amendment to Section 2.3(a) . Section 2.3(a) of the SDWG Investor Rights Agreement is hereby amended and restated in its entirety as set forth in the attached Exhibit B .

      3.  Amendment to Section 2.7 . Section 2.7 of the SDWG Investor Rights Agreement is hereby amended and restated in its entirety as set forth in Exhibit C .

      4.  Amendment to Section 2.9 . Section 2.9 of the SDWG Investor Rights Agreement is hereby amended by adding the following sentence to the end of that provision:

“The Company shall not amend the Hawkeye Registration Rights Agreement or the EIP Registration Rights Agreement in a manner adverse to the Holders without the prior written consent of a majority in interest of the Holders.”

      5.  Governing Law . The parties to this Amendment intend for the laws of the State of Minnesota to govern the validity of this Amendment, the construction of its terms and the interpretation of the rights and duties of the parties, without regard to the conflict of law provisions of such state.

      6.  Counterparts . This Amendment may be executed in any number of counterparts, each of which shall be deemed an original and enforceable against the parties actually executing such counterpart, and all of which together shall constitute one and the same instrument.

      7.  Miscellaneous . Except as specifically amended herein, the SDWG Investor Rights Agreement shall remain in full force and effect, as so amended. Any reference to this “Amendment,” shall include the Recitals set forth in the beginning of this Amendment.

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     This Amendment has been executed by the parties hereto as of the date first set forth above.

EXHIBIT A

AMENDED AND RESTATED ARTICLE 1

     1.  Definitions . For purposes of this Agreement:

          1.1 “ Additional Financing ” means the sale by the Company of additional Units as contemplated by the registration statement on Form SB-2 filed by the Company with the SEC on September 13, 2006, as amended from time to time thereafter.

          1.2 “ Affiliate ” means, with respect to any specified Person, any other Person who or which, directly or indirectly, controls, is controlled by, or is under common control with such specified Person, including without limitation any general partner, officer, director, or manager of such Person.

          1.3 “ Damages ” means any loss, damage, or liability to which a party hereto may become subject under the Securities Act, the Exchange Act, or other federal or state law, insofar as such loss, damage, or liability (or any action in respect thereof) arises out of or is based upon (a) any untrue statement or alleged untrue statement of a material fact contained in any registration statement of the Company, including any preliminary prospectus or final prospectus contained therein or any amendments or supplements thereto; (b) an omission or alleged omission to state therein a material fact required to be stated therein, or necessary to make the statements therein not misleading; or (c) any violation or alleged violation by the indemnifying party (or any of its agents or Affiliates) of the Securities Act, the Exchange Act, any state securities law, or any rule or regulation promulgated under the Securities Act, the Exchange Act, or any state securities law.

          1.4 “ Derivative Securities ” means any securities or rights convertible into, or exercisable or exchangeable for (in each case, directly or indirectly), Units, including options and warrants.

          1.5 “ EIP ” means Ethanol Investment Partners, LLC, a Delaware limited liability company.

          1.6 “ EIP Holder ” means any “Holder” as that term is defined under the Registration Rights Agreement.

          1.7 “ EIP Registration Rights Agreement ” means that certain Registration Rights Agreement dated as of June 25, 2007, between the Company and EIP, as amended.

          1.8 “ Exchange Act ” means the Securities Exchange Act of 1934, as amended, and the rules and regulations promulgated thereunder.

          1.9 “ Excluded Registration ” means (a) a registration of Units in connection with the Additional Financing so long as such registration is declared effective by the SEC no later than February 28, 2007; (b) a registration relating to the sale of securities to employees of

the Company or a subsidiary pursuant to a stock option, stock purchase, or similar plan; or (c) a registration relating to an SEC Rule 145 transaction.

          1.10 “ Form S-1 ” means such form under the Securities Act as in effect on the date hereof or any successor registration form under the Securities Act subsequently adopted by the SEC.

          1.11 “ Form S-2 ” means such form under the Securities Act as in effect on the date hereof or any successor registration form under the Securities Act subsequently adopted by the SEC.

          1.12 “ Form S-3 ” means such form under the Securities Act as in effect on the date hereof or any registration form under the Securities Act subsequently adopted by the SEC that permits incorporation of substantial information by reference to other documents filed by the Company with the SEC.

          1.13 “ GAAP ” means generally accepted accounting principles in the United States.

          1.14 “ Hawkeye ” means Hawkeye Energy Holdings, LLC, a Delaware limited liability company.

          1.15 “ Hawkeye Holders ” means any “Holder” as that term is defined under the Hawkeye Registration Rights Agreement.

          1.16 “ Hawkeye Registration Rights Agreement ” means that certain Registration Rights Agreement dated as of August 28, 2009, between the Company and Hawkeye.

          1.17 “ Holder ” means any holder of Registrable Securities who is a party to this Agreement, including permitted transferees that agree in writing to be bound by and subject to the terms and conditions of this Agreement.

          1.18 “ Initiating Holders ” means, collectively, Holders who properly initiate a registration request under this Agreement.

          1.19 “ IPO ” means the Company’s first underwritten public offering of its Units or other equity securities under the Securities Act.

          1.20 “ Operating Agreement ” means that certain Third Amended and Restated Operating Agreement of the Company dated as of February 1, 2006, as amended from time to time.

          1.21 “ Person ” means any individual, corporation, partnership, trust, limited liability company, association or other entity.

          1.22 “ Registrable Securities ” means (a) the Units issued to SDWG, and any Units acquired by SDWG after the date hereof; and (b) any Units issued as (or issuable upon the conversion or exercise of any warrant, right, or other security that is issued as) a dividend or other distribution with respect to, or in exchange for or in replacement of, the Units referenced in clause (a) above, excluding in all cases, however, any Registrable Securities sold by a Person in a transaction in which the applicable rights under this Agreement are not assigned pursuant to S