Document:

EX-10.5

EXHIBIT 10.5

Amendment No. RI0340T02A

AMENDMENT

TO THE

CONSTRUCTION AND REVOLVING TERM LOAN SUPPLEMENT

THIS AMENDMENT is entered into as of November 20, 2006, between FARM CREDIT SERVICES OF
AMERICA, FLCA (“Farm Credit”) and ABE FAIRMONT, LLC, Fairmont, Nebraska (the “Company”).

BACKGROUND

Farm Credit and ADVANCED BIOENERGY, LLC, Fairmont, Nebraska (“Advanced”) are parties to a
Construction and Revolving Term Loan Supplement dated February 17, 2006 (such agreement, as
previously amended, is hereinafter referred to as the “Supplement”). Further, the Company has
formally assumed all obligations under the Supplement from Advanced. Farm Credit and the Company
now desire to amend certain sections of the Supplement. For that reason, and for valuable
consideration (the receipt and sufficiency of which are hereby acknowledged), Farm Credit and the
Company agree that the following sections of the Supplement are hereby amended to read as follows:

1. The Effective Date in the first paragraph of the Supplement is hereby amended to be June 1,
2007.

2. Section 3 of the Supplement is hereby amended and restated to read as follows:

SECTION 3. Term. The term of the Commitment shall be from the Effective Date hereof (or, if
requested by Company, such earlier date as Agent may, in its sole discretion, authorize in
writing), up to and including December 1, 2016, or such later date as Agent may, in its sole
discretion, authorize in writing.

3. Section 6 of the Supplement is hereby amended and restated to read as follows:

SECTION 6. Promissory Note. The Company promises to repay on the dates set forth below, the
outstanding principal, if any, that is in excess of the listed amounts:

	 	 	 	 	 
	Payment Date	 	Reducing Commitment Amount
	December 1, 2014

	 	$	16,000,000.00	 
	 
	 	 	 	 
	June 1, 2015

	 	$	11,000,000.00	 
	 
	 	 	 	 
	December 1, 2015

	 	$	6,000,000.00	 
	 
	 	 	 	 
	June 1, 2016

	 	$	1,000,000.00	 
	 
	 	 	 	 
	December 1, 2016

	 	$	0.00	 

Provided, however, that if Construction and Term Loan Supplement No. RI0340T01 dated February 17,
2006, as amended, has been repaid prior to its maturity date of May 20, 2014, then repayment for
this loan shall begin on the first day of the month that is six months after the first day of the
month following the repayment of RI0340T01, and reductions in principal as noted above shall occur
every six months thereafter. If any installment due date is not a day on which Agent is open for
business, then such installment shall be due and payable on the next day on which Agent is open for
business. In addition to the above, the Company promises to pay interest on the unpaid principal
balance hereof at the times and in accordance with the provisions set forth in Section 5 hereof.

4. Section 7 of the Supplement is hereby amended and restated to read as follows:

SECTION 7. Prepayment. In addition to the broken funding surcharge provision of the MLA,
prepayment of any outstanding principal balance due to refinancing, or refinancing of any
unadvanced Commitment, up to and including July 1, 2009, will result in a 3% prepayment charge in
addition to any broken funding surcharges which may be applicable, based on the amounts prepaid and
on the total amount of the Commitments in effect at such time.

5. Except as set forth in this amendment, the Supplement, including all amendments thereto, shall
continue in full force and effect as written.

IN WITNESS WHEREOF, the parties have caused this amendment to be executed by their duly
authorized officers as of the date shown above.

FARM CREDIT SERVICES OF AMERICA, FLCA

By: /s/ Shane Fralen

Title: Vice President

ABE FAIRMONT, LLC

By ADVANCED BIOENERGY, LLC, its sole member

By: /s/ Donald Gales

Title: President

11/27/06EX-10.6

EXHIBIT 10.6

ADMINISTRATIVE AGENCY AGREEMENT

THIS ADMINISTRATIVE AGENCY AGREEMENT is entered into as of the 20th day of November, 2006,
among FARM CREDIT SERVICES OF AMERICA, FLCA (“Farm Credit”), COBANK, ACB (“CoBank”) and
ABE FAIRMONT, LLC, Fairmont, Nebraska, a Delaware limited liability company (“Borrower”).

RECITALS

A. Farm Credit intends to extend financing to Borrower, which financing will consist of a
Master Loan Agreement (“MLA”), a Construction and Term Loan Supplement in the amount of
$6,500,000.00 (“Term Loan”) and a Construction and Revolving Term Loan Supplement in the amount of
$4,000,000.00 (“Term Revolver”). The MLA, Term Loan and Term Revolver are hereinafter referred to
as the “Loan Documents.”

B. Farm Credit has agreed to sell a participation interest in the Loan Documents on the
closing of the loans contemplated therein to CoBank (a participation interest up to and including
100%).

C. In recognition of its participation interest and its experience in the types of loans
contemplated herein, CoBank has agreed to undertake the initial drafting of the Loan Documents and
related security documentation (“Security Documents”) and has agreed to undertake the obligations
as administrative agent for these loans.

D. Farm Credit desires to enter into this agreement in order to appoint CoBank as
administrative agent for the Loan Documents and Security Documents. Hereafter, unless otherwise
indicated, “Loan Documents” shall also mean the Security Documents.

NOW, THEREFORE, in consideration of the foregoing and for good and valuable consideration, the
receipt and sufficiency of which is hereby acknowledged by each party, the parties hereto agree as
follows:

1. Appointment, Powers and Immunities of Administrative Agent. Farm Credit hereby appoints and
authorizes CoBank to act as its agent under the Loan Documents and under the Security Documents (in
such capacity the “Administrative Agent”) with such powers as are specifically delegated to such
Administrative Agent by the terms of this Agreement, together with such other powers as are
reasonably incidental thereto. Farm Credit also agrees that as part of CoBank’s duties as
Administrative Agent, CoBank shall, on Farm Credit’s behalf, perform the loan servicing duties of
the “Lead” as such duties are described in the Participation Agreement dated January 12, 1996,
between Farm Credit (formerly Farm Credit Services of the Midlands, FLCA) and CoBank, ACB, as
amended or replaced from time to time (the “Participation Agreement”). The Administrative Agent
shall have no duties or responsibilities except those expressly set forth in this Agreement, the
Loan Documents, and the Participation Agreement, and shall not by reason of this Agreement be a
trustee or fiduciary for Farm Credit; provided, however, the Administrative Agent shall administer
its duties and responsibilities in accordance with its customary practices and procedures with
respect to similar loans for its own account. The Administrative Agent shall not be responsible to
Farm Credit for any recitals, statements, representations or warranties made by Borrower or any
officer or official of Borrower or any other person contained in this Agreement or any other Loan
Document, or in any certificate or other document or instrument referred to or provided for in, or
received by Farm Credit or the Administrative Agent under, this Agreement or any other Loan
Document, or for the value, legality, validity, effectiveness, genuineness, enforceability or
sufficiency of this Agreement or the Loan Documents or any other document or instrument referred to
or provided for herein or therein, or for any failure by Borrower to perform any of its obligations
hereunder or thereunder. The Administrative Agent may employ agents and attorneys-in-fact and shall
not be responsible, except as to money or securities received by it or its authorized agents, for
the negligence or misconduct of any such agents or attorneys-in-fact selected by it with reasonable
care. Neither the Administrative Agent nor any of its respective directors, officers, employees or
agents shall be liable or responsible for any action taken or omitted to be taken by it or them
hereunder or under the Loan Documents or Security Documents or in connection herewith or therewith,
except for its material breach of contract or for its or their own gross negligence or willful
misconduct. Borrower shall pay any fee agreed to by Borrower and the Administrative Agent with
respect to the Administrative Agent’s services hereunder. Borrower acknowledges the appointment of
the Administrative Agent and agrees to be bound by the terms of this Agreement.

2. Reliance by Administrative Agent. The Administrative Agent shall be entitled to rely upon
any certification, notice or other communication (including any thereof by telephone, telex,
facsimile, telegram or cable) believed by it to be genuine and correct and to have been signed or
sent by or on behalf of the proper person or persons, and upon advice and statements of legal
counsel, independent accountants and other experts selected by the Administrative Agent.

3. Defaults. The Administrative Agent shall not be deemed to have knowledge of the occurrence
of a Potential Default or Event of Default, as those terms are defined in the MLA, unless the
Administrative Agent has received notice from Farm Credit or Borrower specifying such Potential
Default or Event of Default and stating that such notice is a “Notice of Default.” In the event
that the Administrative Agent receives such a Notice of Default from Borrower, the Administrative
Agent shall give prompt notice thereof to Farm Credit. The Administrative Agent shall take such
action with respect to such Potential Default or Event of Default which is continuing as determined
by the parties under the Participation Agreement. The Administrative Agent shall not be required to
take any action which it determines to be contrary to Law.

4. Indemnification of Administrative Agent. Farm Credit agrees to indemnify the Administrative
Agent (to the extent not reimbursed under the applicable provisions of the Loan Documents), for its
pro rata participation share of any and all liabilities, obligations, losses, damages, penalties,
actions, judgments, suits, costs, expenses or disbursements of any kind and nature whatsoever
(including reasonable attorneys’ fees) which may be imposed on, incurred by or asserted against the
Administrative Agent in any way relating to or arising out of Loan Documents, or any other
documents contemplated by or referred to therein, or the transactions contemplated hereby or
thereby (including, without limitation, the costs and expenses which Borrower is obligated to pay
under the MLA) or under the applicable provisions of any of the Loan Documents or the Security
Documents or the enforcement of any of the terms hereof or thereof or of any such other documents
or instruments; provided that Farm Credit shall not be liable for any of the foregoing to the
extent they arise from material breach of this Agreement or from the gross negligence or willful
misconduct of the Administrative Agent or its directors, officers, employees or agents.

5. Non-Reliance on Administrative Agent. Farm Credit agrees that it has, independently and
without reliance on the Administrative Agent, and based on such documents and information as it has
deemed appropriate, made its own credit analysis of Borrower and the decision to enter into this
Agreement and either originate the loans and/or purchase a participation in the Loan Documents and
that it will, independently and without reliance upon the Administrative Agent, and based on such
documents and information as it shall deem appropriate at the time, continue to make its own
analysis and decisions in taking or not taking action under this Agreement or the Loan Documents.
The Administrative Agent shall be required to keep itself informed as to the performance or
observance by Borrower of the Loan Documents or any other document referred to or provided for
herein or therein and to inspect the properties or books of Borrower. The Administrative Agent
shall have the duty and responsibility to provide Farm Credit with any credit or other information
concerning the affairs, financial condition or business of Borrower which may come into the
possession of the Administrative Agent. The Administrative Agent shall not be required to file this
Agreement, the Loan Documents or any document or instrument referred to herein or therein, for
record or give notice of this Agreement or any other Loan Document or any document or instrument
referred to herein or therein, to anyone. Farm Credit acknowledges and agrees that the
Administrative Agent only has the duties and responsibilities explicitly set forth herein and in
the Loan Documents and Security Documents.

6. Failure of Administrative Agent to Act. Except for action expressly required of the
Administrative Agent hereunder, the Administrative Agent shall in all cases be fully justified in
failing or refusing to act hereunder unless it shall have received further assurances (which may
include cash collateral) of the indemnification obligations of Farm Credit under Section 4 above in
respect of any and all liability and expense which may be incurred by it by reason of taking or
continuing to take any such action.

7. Resignation or Removal of Administrative Agent. Subject to the appointment and acceptance
of a successor Administrative Agent, as provided below, the Administrative Agent may resign at any
time by giving written notice thereof to Farm Credit and Borrower. Upon any such resignation or
removal, Farm Credit shall have the right to appoint a successor Administrative Agent which must be
located in the United States of America. If no successor Administrative Agent shall have been so
appointed and shall have accepted such appointment within thirty (30) days after the retiring
Administrative Agent’s giving of notice of resignation, then the retiring Administrative Agent may,
on behalf of Farm Credit, appoint a successor Administrative Agent which must be located in the
United States of America. Farm Credit or the retiring Administrative Agent, as the case may be,
shall upon the appointment of a successor Administrative Agent promptly so notify Borrower. Upon
the acceptance of any appointment as Administrative Agent hereunder by a successor Administrative
Agent, such successor Administrative Agent shall thereupon succeed to and become vested with all
the rights, powers, privileges and duties of the retiring Administrative Agent and the retiring
Administrative Agent shall be discharged from its duties and obligations hereunder, except for any
liability arising from gross negligence, willful misconduct or material breach of this Agreement.
After any retiring Administrative Agent’s resignation hereunder as Administrative Agent, the
provisions of this Agreement shall continue in effect for its benefit in respect of any actions
taken or omitted to be taken by it while it was acting as Administrative Agent.

8. Amendments Concerning Agency Function. The Administrative Agent shall not be bound by any
waiver, amendment, supplement or modification of this Agreement or the Loan Documents or Security
Documents which affects its duties hereunder or thereunder unless it shall have given its prior
consent thereto.

9. Liability of Administrative Agent. Except as otherwise provided in the Loan Documents, the
Security Documents and herein, the Administrative Agent shall not have any liabilities or
responsibilities to Borrower on account of the failure of Farm Credit to perform its obligations
hereunder or to Farm Credit on account of the failure of Borrower to perform their respective
obligations hereunder or under the Loan Documents or Security Documents.

10. Transfer of Agency Function. Without the consent of Borrower, the Administrative Agent may
at any time or from time to time transfer its functions as Administrative Agent hereunder to any of
its offices located in the United States of America, provided that the Administrative Agent shall
promptly notify Borrower.

11. Non-Receipt of Funds by Administrative Agent.

A. Unless Administrative Agent shall have received notice from Farm Credit prior to the date
on which Farm Credit is to provide funds to Administrative Agent for an Advance to be made by Farm
Credit that Farm Credit will not make available to Administrative Agent such funds, Administrative
Agent may assume that Farm Credit has made such funds available to Administrative Agent on the date
of such Advance in accordance with the terms of this Agreement and Administrative Agent in its sole
discretion may, but shall not be obligated to, in reliance upon such assumption, make available to
Borrower on such date a corresponding amount. If and to the extent Farm Credit shall not have made
such funds available to Administrative Agent, Farm Credit agrees to repay Administrative Agent
forthwith on demand such corresponding amount together with interest thereon, for each day from the
date such amount is made available to Borrower until the date such amount is repaid to
Administrative Agent, at the customary rate set by Administrative Agent for the correction of
errors among banks for three (3) Banking Days and thereafter at the “Base Rate” (as that term is
used and defined in the Loan Documents). If Farm Credit shall repay to Administrative Agent such
corresponding amount, such amount so repaid shall constitute Farm Credit’s Advance for purposes of
this Agreement, the Loan Documents and/or Security Documents. If Farm Credit does not pay such
corresponding amount forthwith upon Administrative Agent’s demand therefore, Administrative Agent
shall promptly notify Borrower, and Borrower shall immediately pay such corresponding amount to
Administrative Agent with the interest thereon, for each day from the date such amount is made
available to Borrower until the date such amount is repaid to Administrative Agent, at the rate of
interest applicable at the time to such proposed Advance.

B. Unless Administrative Agent shall have received notice from Borrower prior to the date on
which any payment is due hereunder that Borrower will not make such payment in full, Administrative
Agent may assume that Borrower has made such payment in full to Administrative Agent on such date
and Administrative Agent in its sole discretion may, but shall not be obligated to, in reliance
upon such assumption, cause to be distributed to Farm Credit on such due date an amount equal to
the amount then due Farm Credit. If and to the extent Borrower shall not have so made such payment
in full to Administrative Agent, Farm Credit shall repay to Administrative Agent forthwith on
demand such amount distributed to Farm Credit together with interest thereon, for each day from the
date such amount is distributed to Farm Credit until the date Farm Credit repays such amount to
Administrative Agent at the customary rate set by Administrative Agent for the correction of errors
among banks for three (3) Banking Days and thereafter at the Base Rate.

12. Amendments, Etc. No amendment, modification, termination, or waiver of any provision of
this Agreement or the Loan Documents or Security Documents to which Borrower is a party, shall in
any event be effective to modify or change the duties or rights of the Administrative Agent unless
the same shall be in writing and signed by the Banks and the Administrative Agent and have the
consent and signature of the Borrower.

13. Notices. All notices or communications hereunder shall be in writing and shall be deemed
duly given upon delivery if personally delivered or sent by telegram or facsimile transmission, or
three (3) days after mailing if sent by express, certified or registered mail, to the parties at
the following addresses (or such other address for a party as shall be specified by like notice):

Farm Credit Services of America,
FCLA P.O. Box 2409

Omaha, Nebraska 68103-2409

Attention: Kathy Frahm
Telephone: (402)
348-3669 Facsimile:
(402) 661-3669

CoBank, ACB

11422 Miracle Hills Drive,
Suite 300 Omaha, Nebraska 68
154-4404

Attention: Tom Houser

Telephone: (402) 492-2013

Facsimile: (402) 492-2001

ABE Fairmont, LLC
137 North 8th
Street Geneva,
Nebraska 68361

Attention: Don Gales

Telephone: (402) 759-3776

Facsimile: (402) 759-3774

14. Attorney’s Fees. The prevailing party in any action or other proceeding to enforce its
rights under this Agreement, shall be entitled to its costs of suit, and reasonable attorneys’
fees, in addition to all other recovery or relief to which it may be entitled.

15. Governing Law. This Agreement shall be governed by and construed in accordance with the
laws of the State of Colorado.

16. Counterparts. This Agreement may be executed in any number of counterparts and by
different parties to this Agreement in separate counterparts, each of which, when so executed,
shall be deemed to be an original and all of which taken together shall constitute one and the same
Agreement.

IN WITNESS WHEREOF, the parties hereto have caused the execution of this Agreement as of the
date first above written.

FARM CREDIT SERVICES OF AMERICA, FLCA

By: /s/ Shane Fralen

Title: Vice President

ABE FAIRMONT, LLC

By ADVANCED BIOENERGY, LLC, its sole member

By: /s/ Donald Gales

Title: President

CoBANK, ACB

	 	 	 
	By:

	 	/s/ Janice P. Haines
	 

	 	 
	Title:

	 	Assistant Corporate Secretary

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