Exhibit 10.1

ADVANCED BIOENERGY, LLC

8000 Norman Center Dr., Suite 610

Bloomington, MN 55437

Letter Agreement

Dated as of January 18, 2013

Mr. Richard R. Peterson

Chief Executive Officer and Chief Financial Officer

Advanced BioEnergy, LLC

8000 Norman Center Drive, Suite 610

Bloomington, MN 55437

Dear Rich:

We are pleased to inform you that the compensation committee of ABE has recommended, and the board of directors of ABE (the “Board”) has approved, the following compensation package for you:

Advanced BioEnergy

January 18, 2013

Page 2

The Board approved the issuance of the Change in Control Units to you notwithstanding the fact that your employment with ABE was not terminated in connection with a Change in Control, as had been required by the Change of Control Agreement.

You will be awarded Unit Appreciation Rights (“UAR”) with respect to 200,000 Units. As set forth in the Unit Appreciation Right Agreement (whose language is controlling), the UAR will vest 1/18 per month over an 18 month period beginning December 7, 2012 and be paid in cash upon such time as ABE sells all or substantially all the assets of the South Dakota plants.

Advanced BioEnergy

January 18, 2013

Page 3

The UAR will expire four years following the date of grant. The UAR will be issued to you for no consideration and will have a grant price of $1.15 per UAR at the time of the grant; provided, however, the grant price for the UAR will be reduced by any distribution received by the Company’s unit holders from the Escrow Funds or the $10 Million of cash reserved by the Company in connection with the Fairmont Sale. In order to ensure compliance under Section 162(m) of the Internal Revenue Code, the issuance of the UAR to you is subject to approval by the Company’s Unit holders by a majority of votes cast at a member meeting within twelve (12) months of the date of the grant, and, if not approved, the UAR will be cancelled and have further no force and effect.

Except as expressly noted in this Letter Agreement, your Employment Agreement will not be modified and will remain in full force and effect. Your base salary will continue at $285,000 per year. During the next eighteen months, we expect you to take appropriate steps to (i) reduce operations in the Minneapolis office; (ii) wind down the Fairmont subsidiary; and (iii) continue to drive value in South Dakota assets.

Your Employment Agreement will be amended to have a guaranteed extended term of eighteen (18) months from December 7, 2012 (“the Extended Term”). If you are terminated by ABE during that Extended Term for any reason other than “for cause” (as defined in your Employment Agreement), you will be entitled to your salary to which you would otherwise have been entitled during the Extended Term (the “Guaranteed Salary”). If you voluntarily resign for any reason, including “good reason” (as defined in your Employment Agreement) during the Extended Term, you will not be entitled to your Guaranteed Salary and you will forfeit any severance payments to which you may have otherwise been entitled under your Employment Agreement.

The Company and you agree that the Cost-Saving Incentive Bonus, the Escrow Incentive Bonus, and the grant of the UAR are being awarded to you in lieu of any other Annual Performance Bonus for fiscal 2013 under Section 3(f) of your Employment Agreement, and you will not be entitled to any other Annual Performance Bonus for fiscal 2013.

Sincerely,

Scott A. Brittenham

Chairman of the Board of Directors

Advanced BioEnergy, LLC

Advanced BioEnergy

January 18, 2013

Page 4

Exhibit A

Criteria for Peterson Annual Performance Bonus for 2012

Peterson’s Annual Performance Bonus for fiscal year 2012 was based upon the following criteria:

Exhibit 10.2

AMENDMENT NO. 1 TO SECOND AMENDED AND RESTATED

EMPLOYMENT AGREEMENT

This Amendment No. 1 to Second Amended and Restated Employment Agreement (this “Amendment”) is entered into on this 18th day of January, 2013 by and between Advanced BioEnergy, LLC, a Delaware limited liability company (the “Company”), and Richard Peterson, a resident of Minnesota (“Employee”). Capitalized terms used herein but not otherwise defined have the meanings set forth in the Original Agreement (as defined below).

RECITALS

WHEREAS , Employee entered into a Second Amended and Restated Employment Agreement with the Company, dated May 11, 2011 (the “Original Agreement”); and

WHEREAS , the Company and Employee wish to make certain changes to the Original Agreement.

NOW, THEREFORE , for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows:

AMENDMENT

1. Employment; Term . Section 1 of the Original Agreement shall be replaced in its entirety with the following:

“Subject to all terms and conditions hereof, the Company will employ Employee, and Employee will continue to serve the Company and perform services for the Company, for a term ending on June 7, 2014 (the “Term”), or until Employee’s employment terminates under Section 11.”

2. Payments Upon Termination of Employment . Section 12 of the Original Agreement shall be replaced in its entirety with the following:

“12. Payments Upon Termination of Employment.

(a) Payments Upon Termination by the Company Without Cause. If Employee’s employment with the Company is terminated by the Company during the Term for any reason other than for “Cause” (as defined below), then Employee shall in such case receive from Company the following severance pay and benefits:

(1) The Company will pay Employee his base salary amount in effect immediately prior to the Termination Date (which base salary will not be lower than $285,000 per year) through the end of the Term (the “Guaranteed Salary”) in accordance with the Company’s normal payroll policies and procedures.

(2) The Company will pay Employee severance pay in an aggregate amount equal to one hundred four (104) weeks of Employee’s weekly base salary amount immediately prior to the Termination Date (which base salary will not be lower than $285,000 per year) (“Severance Payment”), payable over two years in equal installments in accordance with the Company’s regular payroll practices, with the first payment beginning no earlier than the expiration of all applicable rescission periods provided by law and no later than forty-five (45) calendar days following the Termination Date; provided that if the 45 day period begins in one taxable year and ends in a second taxable year, the Company will begin payment in the second taxable year.

(3) As part of the Company’s obligation to provide Employee with COBRA coverage, provided Employee is eligible for and takes all steps necessary to continue his and his family’s then-applicable health, dental, disability and life insurance coverage with the Company following the Termination Date, the Company will continue to provide such coverage under the same terms and conditions as then made available to other Company employees and their families (the employer- and employee-portions being the same as for then-current Company employees) for up to one year following the Termination Date. The Company shall be entitled to cease providing any health, dental, disability, or life insurance benefits prior to one year after the Termination Date if Employee becomes eligible for group health, dental, disability or life insurance coverage (as applicable) from any other employer. Once Employee has become eligible for comparable group health, dental, disability or life insurance coverage from any other such employer, Employee shall promptly and fully disclose this fact to the Company in writing and shall be liable to repay any amounts to the Company that should have been so mitigated or reduced but for Employee’s failure or unwillingness to make such disclosure. In the event applicable provisions of the Patient Protection and Affordable Care Act of 2012, as amended, shall become effective such that the subsidy for COBRA premiums would be deemed discriminatory, then this Paragraph 3 shall become void and the Company shall have no further obligation under this Paragraph 3, except as required by applicable provisions of COBRA.

(4) Each payment pursuant to this Section 12 will constitute a separate payment under Internal Revenue Code Section 409A.

(b) Payments Upon Termination By Employee . If Employee’s employment with the Company is terminated by Employee during the Term for any reason, then Employee shall in such case receive from the Company only his base salary through the Termination Date and shall not be entitled to any payments under Section 12(a) hereof.

(c) Wages Due . If Employee’s employment with the Company is terminated by the Company for Cause, then the Company will pay to Employee Employee’s base salary through the Termination Date and shall have no obligation to provide the Guaranteed Salary, any severance pay or benefits under this Agreement to Employee.

(d) Payments Upon Disability or Death . Upon Employee’s Disability or death during the Term, the Company shall pay Employee or Employee’s estate, as applicable, the Severance Payment, but Employee or Employee’s estate, as applicable, shall not be entitled to receive the Guaranteed Salary.

(e) Limitations on Severance Pay . Notwithstanding the foregoing provisions of this Section 12, the obligation of the Company to make any of the termination payments to Employee under Sections 12(a) or 12(d) of this Agreement is contingent upon Employee’s execution of a full and valid release of claims arising out of his employment or the termination of that employment in favor of the Company, its officers, directors, agents, employees, successors, assigns and affiliates. Execution of such a release and the expiration of any applicable rescission period, following such execution, is a condition precedent to the Company’s obligation to make any of the termination payments set forth in this Agreement.

(f) If, as of the Termination Date, Employee is a “specified employee” under Section 409A(a)(2)(B)(i) of the Code, and if any payments that Employee is entitled to receive hereunder may not be made at the time contemplated by the terms of this Agreement without causing Employee to be subject to the additional tax imposed by Section 409A of the Code, then any such payments under this Agreement that would have been paid during the period six months after Termination Date shall be held and paid in a lump sum on the first day of the seventh month following the Termination Date (without interest or earnings). Such deferral, if any, shall have no effect on any payments scheduled following the period six months after the Termination Date.

(g) For purposes of this Agreement, “Cause” shall mean:

(1) an act of dishonesty undertaken by Employee and intended to result in personal gain or enrichment of Employee or another at the expense of the Company or its Affiliates;

(2) unlawful conduct or gross misconduct by Employee, whether on the job or off the job, that, in either event, is publicly detrimental to the reputation or goodwill of the Company;

(3) the conviction of Employee of a felony, or Employee’s entry of a no contest or nolo contendre plea to a felony;

(4) persistent failure of Employee to perform Employee’s material duties and responsibilities hereunder or to meet reasonable performance objectives set by the Board, as applicable, from time to time, which failure is willful and deliberate on Employee’s part and has not been cured by Employee within fifteen (15) days after written notice thereof to Employee from the Company;

(5) willful and deliberate breach by Employee of his fiduciary obligations as an officer or director of the Company; or

(6) material breach of any terms or conditions of this Agreement by Employee which breach has not been cured by Employee within fifteen (15) days after written notice thereof to Employee from the Company.

For the purposes of this Section 12(g), no act or failure to act on Employee’s part shall be considered “dishonest,” “willful” or “deliberate” unless done or omitted to be done by Employee in bad faith and without reasonable belief that Employee’s action or omission was in the best interests of the Company. Any act, or failure to act, based upon authority given pursuant to a resolution duly adopted by the Board shall be conclusively presumed to be done, or omitted to be done, by Employee in good faith and in the best interests of the Company.

3. Employment Beyond Term . Notwithstanding any other provision in the Original Agreement or this Amendment to the contrary, if Employee’s employment with the Company extends beyond the Term, Employee shall not be entitled to the Severance Payment.

4. Change in Control . Appendix A to the Original Agreement is hereby deleted in its entirety.

5. Unit Appreciation Right . Nothing in this Amendment affects Employee’s rights under the Unit Appreciation Right dated as of January 18, 2013.

6. Other Matters . Except as specifically amended herein, all terms and conditions of the Original Agreement remain in full force and effect.

[Signature page contained on following page.]

IN WITNESS WHEREOF, the parties have executed this Amendment on the day and year first written above.

Advanced BioEnergy, LLC (the “Company”) is pleased to inform you that you have been granted Unit Appreciation Rights (“UARs”) as set forth above (this “Award”). The terms of this Award are as follows:

1. Vesting .

(a) The UARs shall vest 1/18 ^th  per month over an 18 month period, beginning on December 7, 2012 (the “Qualifying Period”), such that 1/18 ^th of the UARs have vested as of the Date of Grant, 2/18 of the UARs will vest on February 7, 2013 and thereafter 1/18 of the UARs will vest on the 7th of each month; provided however, that you have been continuously employed by the Company during the preceding month for such portion of the UARs to vest.

(b) The vested UARs shall become automatically payable on the date (the “Payment Date”) which is the earliest of (i) the closing on the sale of all or substantially all of the assets (the “SD Assets”) of ABE South Dakota, LLC (“ABE South Dakota”), (ii) the occurrence of a “Change in Control,” as defined in Appendix A to this Award, of the Company, (iii) your death, or (iv) your termination of employment due to a “Disability,” as defined in Section 11 of your Employment Agreement.

(c) If, on any date during the Qualifying Period, you are terminated by the Company “for cause” (as defined in your Employment Agreement), the UARs shall automatically and immediately be forfeited and cancelled without payment therefor on such date.

2. Expiration . Notwithstanding any other provision of this Award to the contrary, the UARs shall immediately expire and be of no further force and effect if the Unit holders do not approve of the UAR within twelve (12) months after the date of this Award in accordance with Section 162(m) of the Internal Revenue Code and regulations promulgated thereunder, regardless of whether a Payment Date has been deemed to have occurred.

3. No Right to Continued Employment . Nothing in this Award shall confer any right on you to continue in the Company’s employ or service or affect any right which the Company has to terminate such employment or retention.

4. UAR Payment .

(a) No later than five (5) business days after the Payment Date, the Company will pay you, with respect to each UAR, an amount equal to the excess, if any, of (a) the fair market value on the Payment Date of a Unit, on a fully diluted basis, as if the UARs were outstanding Units on such date, over (b) the grant price per UAR, which price equals $1.15 per Unit (the “Grant Price”).

(b) The Grant Price will be reduced by any distribution received by the Unit holders of the Company from (i) the proceeds of the escrow account (the “Escrow Funds”) established pursuant to that certain Escrow Agreement, dated December 7, 2012, by and among ABE Fairmont, LLC, the Company, Flint Hills Resources Fairmont, LLC and Wells Fargo Bank, National Association in connection with the sale of the Company’s Fairmont, Nebraska ethanol plant (the “Asset Sale”) or (ii) the amount reserved by the Company from the proceeds of the Asset Sale (any such distribution set forth in clauses (i) and (ii) above, a “Grant Price Reducing Distribution”). Any Grant Price Reducing Distribution shall reduce the Grant Price by the amount of such Grant Price Reducing Distribution until the Grant Price is reduced to $0, at which point, any remaining amount per Unit of the Grant Price Reducing Distribution shall be payable as a distribution to Grantee.

(c) Payment with respect to the UAR shall be made in cash, subject to all applicable tax withholding.

(d) The determination of fair market value of a Unit shall be made in good faith in the sole discretion of the Compensation Committee of the board of directors of the Company, which determination shall be final and binding on all parties. In the event the Grant Price per UAR exceeds the fair market value per Unit on the Payment Date, then all UARs shall be immediately cancelled without payment therefor, and thereafter you shall have no right to any further payment under this Agreement.

(e) For purpose of Internal Revenue Code Section 409A, the Company and you agree that in establishing the fair market value of $1.15 per Unit, the Company is including in fair market value the $22.5 Million referred to in Section 4(b) above. The Company and you also agree that a portion of your overall compensation, apart from this UAR, is based upon the Company’s receipt of the Escrow Funds, and it is appropriate to reduce the Grant Price to reflect the value of the Company without regard to these items. The Company and you also agree that the board of directors of the Company, or the compensation committee thereof, will reduce the Grant Price in the event that the Escrow Funds are not received by the Company and distributed to the Company’s Unit holders. The Company and you also agree, as set forth in Section 7 of this Award, that the board of directors of the Company, or the compensation committee thereof, has power to make any other adjustments it believes appropriate and necessary to give effect to the intent of the parties to this Award.

5. Transferability . None of the UARs are transferable (by operation of law or otherwise) by you, other than by will or the laws of descent and distribution. If, in the event of your divorce, legal separation or other dissolution of your marriage, your former spouse is awarded ownership of, or an interest in, all or part of the UARs covered by this Award, this Award shall automatically and immediately be forfeited and cancelled in full without payment on such date.

6. Governing Law . This Award shall be governed by, and construed in accordance with, the laws of the State of Minnesota, without regard to conflicts of laws principles thereof.

7. Changes in Capitalization . In the event of any reorganization, merger, consolidation, recapitalization, liquidation, Unit dividend, Unit split, combination of Units, rights offering, or extraordinary dividend or divestiture (including a spin-off), or any other change in the structure or Units of the Company, including any conversion by the Company into a corporate form, the Compensation Committee (or if the Company does not survive any such transaction, the board of directors or an authorized committee of the board of directors of the surviving company) shall, without your consent, make such adjustments as it determines in its discretion to be appropriate as to the number of UARs or the Grant Price per UAR in order to prevent dilution or enlargement of your rights hereunder.

8. Unfunded Status . Other than as provided in Sections 4 and 7 above, you shall not be entitled to any voting rights, to receive any dividends with respect to your UARs or to have the value of your UARs credited or increased as a result of any other distribution with respect to the Units of the Company. You will not have any interest in any particular assets of the Company by reason of your UARs, and no provision will be made with respect to segregating assets of the Company for payment of the value of your UARs.

9. General . This Award shall be binding upon and inure to the benefit of any successor or successors of the Company. The invalidity or unenforceability of any provision of this Award shall not affect the validity or enforceability of any other provision of this Award. Except as otherwise expressly set forth in this Award, any term of this Award may be amended and the observance of any term of this Award may be waived (either generally or in a particular instance and either retroactively or prospectively) only upon the written consent of the parties hereto. No waivers of or exceptions to any term, condition or provision of this Award, in any one or more instances, shall be deemed to be, or construed as, a further or continuing waiver of any such term, condition or provision.

[SIGNATURE PAGE FOLLOWS]

IN WITNESS WHEREOF, the parties have executed this Unit Appreciation Right Agreement as of the 18th day of January, 2013.

Appendix A

“Change in Control” for purposes of this Award shall mean the occurrence of any one or more of the following:

(1) the acquisition, during any 12 consecutive month period that ends subsequent to the Date of Grant of this Award (“Effective Date”), by any “person” (within the meaning of section 13(d)(3) or 14(d)(2) of the Exchange Act) (an “Acquirer”) of ownership (determined taking into account the ownership attribution rules of Section 318(a) of the Code) of membership interests of the Company possessing 30% or more of the total voting power of the then outstanding membership interests of the Company; provided that for purposes of this paragraph (1):

(a) any membership interests of the Company owned by the Acquirer prior to the start of the applicable 12 consecutive month period shall not be counted toward the 30% threshold specified above; and

(b) an acquisition shall not constitute a Change in Control pursuant to this paragraph (1) if: (i) prior to the acquisition, the Acquirer owns membership interests of the Company possessing more than 50% of the total fair market value or total voting power of the then outstanding membership interests of the Company; (ii) the acquisition is by the Company or a subsidiary of the Company; (iii) the acquisition is by an employee benefit plan (or related trust) sponsored or maintained by the Company or one or more of its subsidiaries; (iv) the acquisition is by Grantee or any group that includes Grantee; or (v) the acquisition is by a surviving or acquiring entity in connection with a Business Combination described in clause (4)(a) below;

(2) the acquisition by an Acquirer of membership interests of the Company that, together with membership interests already held by such Acquirer, constitutes more than 50% of the total fair market value or total voting power of the membership interests of the Company, other than an acquisition by an Acquirer who, prior to the acquisition, owned more than 50% of the total fair market value or total voting power of the membership interests of the Company;

(3) the replacement, during any 12 consecutive month period that ends subsequent to the Effective Date, of a majority of the members of the Board with members whose appointment or election is not endorsed by a majority of the members of the Board before the date of the appointment or election;

(4) the consummation of a merger or consolidation of the Company with or into another entity, a statutory share exchange or a similar business combination involving the Company (each, a “Business Combination”) which, subsequent to the Effective Date, has been approved by the Unit holders of the Company, other than (a) a Business Combination where the holders of membership interests of the Company immediately before the Business Combination own, directly or indirectly, 65% or more of the total voting power of all the outstanding equity securities of the surviving or acquiring entity resulting from such Business Combination, or (b) a Business Combination where Grantee or a group that includes Grantee owns, directly or indirectly, 30% or more of the total value or voting power of all the outstanding equity interests of the surviving or acquiring entity resulting from such Business Combination; or

(5) the acquisition, during any 12 consecutive month period that ends subsequent to the Effective Date, by an Acquirer of assets of the Company with a total gross fair market value (determined without regard to any liabilities associated with such assets) equal to more than 40% of the total gross fair market value of all assets of the Company immediately prior to the acquisition, other than an acquisition (a) by a holder of membership interests in the Company immediately prior to such acquisition in exchange for its Company membership interests, (b) by an entity 65% or more of the total voting power of which is owned, directly or indirectly, by the Company, (c) by a person or group (within the meaning of 26 CFR § 1.409A-3(i)(5)(vii)(C)) that owns, directly or indirectly, 65% or more of the total voting power of all outstanding membership interests of the Company, (d) by an entity 65% or more of the total voting power of which is owned, directly or indirectly, by a person or group described in the immediately preceding clause (c), or (e) by a corporation or other entity 30% or more of the total value or voting power of which is owned, directly or indirectly, by Grantee or a group that includes Grantee.