Document:

EX-10.1

EXHIBIT 10.1

MASTER LOAN AGREEMENT

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

BACKGROUND

From time to time Farm Credit may make loans to the Company. In order to reduce the amount of
paperwork associated therewith, Farm Credit and the Company would like to enter into a master loan
agreement. For that reason, and in consideration of Farm Credit making one or more loans to the
Company, Farm Credit and the Company agree as follows:

SECTION 1. Supplements. In the event the Company desires to borrow from Farm Credit and the
Company has satisfied the conditions precedent set forth in Section 7 of this Master Loan Agreement
(the “MLA”), Farm Credit will lend to the Company, (or in the event Farm Credit and the Company
desire to consolidate any existing loans hereunder) pursuant to a Supplement to this agreement (a
“Supplement”) and other provisions hereof. Each Supplement will set forth the amount of the loan,
the purpose of the loan, the interest rate or rate options applicable to that loan, the repayment
terms of the loan, and any other terms and conditions applicable to that particular loan. Each loan
will be governed by the terms and conditions contained in this agreement and in the Supplement
relating to the loan.

SECTION 2. Sale of Participation Interests and Appointment of Administrative Agent. The
Company acknowledges that concurrent with the execution of this MLA and related Supplements, Farm
Credit is selling a participation interest in this MLA and Supplements executed concurrently
herewith to CoBank, ACB (“CoBank”) (up to a 100% interest). Pursuant to an Administrative Agency
Agreement dated November 20, 2006, (“Agency Agreement”), Farm Credit and CoBank appointed CoBank to
act as Administrative Agent (“Agent”) to act in place of Farm Credit hereunder and under the
Supplements and any security documents to be executed thereunder. All funds to be advanced
hereunder shall be made by Agent, all repayments by the Company hereunder shall be made to Agent,
and all notices to be made to Farm Credit hereunder shall be made to Agent. Agent shall be solely
responsible for the administration of this agreement, the Supplements and the security documents to
be executed by the Company thereunder and the enforcement of all rights and remedies of Farm Credit
hereunder and thereunder. Company acknowledges the appointment of the Agent and consents to such
appointment.

SECTION 3. Availability. Loans will be made available on any day on which Agent and the
Federal Reserve Banks are open for business upon the telephonic or written request of the Company.
Requests for loans must be received no later than 12:00 Noon Company’s local time on the date the
loan is desired. Loans will be made available by wire transfer of immediately available funds to
such account or accounts as may be authorized by the Company. The Company shall furnish to Agent a
duly completed and executed copy of a CoBank Delegation and Wire and Electronic Transfer
Authorization Form of the Agent, and Agent shall be entitled to rely on (and shall incur no
liability to the Company in acting on) any request or direction furnished in accordance with the
terms thereof.

SECTION 4. Repayment. The Company’s obligation to repay each loan shall be evidenced by the
promissory note set forth in the Supplement relating to that loan or by such replacement note as
Agent shall require. Agent shall maintain a record of all loans, the interest accrued thereon, and
all payments made with respect thereto, and such record shall, absent proof of manifest error, be
conclusive evidence of the outstanding principal and interest on the loans. All payments shall be
made by wire transfer of immediately available funds, by check, or by automated clearing house or
other similar cash handling processes as specified by separate agreement between the Company and
Agent. Wire transfers shall be made to ABA No. 307088754 for advice to and credit of CoBank (or to
such other account as Agent may direct by notice). The Company shall give Agent telephonic notice
no later than 12:00 Noon Company’s local time of its intent to pay by wire and funds received after
3:00 p.m. Company’s local time shall be credited on the next business day. Checks shall be mailed
to CoBank, ACB, Department 167, Denver, Colorado 80291-0167 (or to such other place as Agent may
direct by notice). Credit for payment by check will not be given until the later of: (a) the day on
which Agent receives immediately available funds; or (b) the next business day after receipt of the
check.

SECTION 5. Capitalization. The Company agrees to purchase voting (Class D) or non-voting
(Class E) stock in Farm Credit Services of America, ACA ($1,000.00 worth of stock consisting of at
least 200 shares of $5.00 par value stock) as required under the policy of Farm Credit at the time
of acquisition. Farm Credit policy may change from time to time. Farm Credit shall have a first
lien on the stock for payment of any liability of the Company to Farm Credit. Said stock shall be
owned as follows:

Owner Name: ABE Fairmont, LLC SSN/TIN: 20-5736411

The Company authorizes and appoints the following to act on behalf of the Company, to vote the
Class D stock, and to accept, receive and receipt for any dividends declared on the stock:

Revis L. Stephenson, III, voter

SECTION 6. Security. The Company’s obligations under this agreement, all Supplements (whenever
executed), and all instruments and documents contemplated hereby or thereby, shall be secured by a
statutory first lien on all equity which the Company may now own or hereafter acquire in Farm
Credit. In addition, the Company agrees to grant to Farm Credit, by means of such instruments and
documents as Agent shall reasonably require, a first lien (subject only to exceptions approved in
writing by Agent) on all personal property of the Company, and on all real property of the Company,
whether now existing or hereafter acquired. As additional security for those obligations: (i) the
Company agrees to grant to Farm Credit, by means of such instruments and documents as Agent shall
reasonably require, a first priority lien on such of its other assets, whether now existing or
hereafter acquired, as Agent may from time to time require; and (ii) the Company agrees to grant to
Farm Credit, by means of such instruments and documents as Agent shall require, a first priority
lien on all realty which the Company may from time to time acquire after the date hereof. Farm
Credit may at its discretion assign collateral to the Agent under the Agency Agreement.

SECTION 7. Conditions Precedent.

(A) Conditions to Initial Supplement. Farm Credit’s obligation to extend credit under the
initial Supplement hereto is subject to the conditions precedent that Agent receive, in form and
content satisfactory to Agent, each of the following:

(i) This Agreement, Etc. A duly executed copy of this agreement and all instruments and
documents contemplated hereby.

(ii) Security Agreement. A security agreement granting to Farm Credit a first lien (subject
only to exceptions approved in writing by Agent) on all personal property of the Company, whether
now owned or hereafter acquired.

(iii) Mortgage/Deed of Trust. A mortgage or deed of trust granting to Farm Credit a first
lien (subject only to exceptions approved in writing by Agent) on the Company’s Property (as that
term is defined in the applicable Supplements) located near Fairmont, Nebraska.

(iv) Title Commitment/Policy. A commitment from a title insurance company acceptable to Agent
to issue an ALTA lender’s policy of title insurance in the face amount of $95,000,000.00 insuring
the Company’s Mortgage or Deed of Trust to Farm Credit as a first priority lien on the property
encumbered thereby, subject only to exceptions approved in writing by Agent. The Company agrees to
pay the cost of such commitment and the related policy, together with such endorsements as may be
reasonably requested by Agent, and also agrees that if, for any reason, a final policy is not
issued by the date that is ninety (90) days after the date of this agreement or such later date as
may be agreeable to Agent, then an “Event of Default” shall be deemed to have occurred under this
agreement.

(v) Insurance. Certificates from the insurance carrier for the general contractor or
contractors (and if the Company is not adequately insured therein, from the Company’s insurance
carrier) evidencing workers’ compensation and liability insurance (including contractual
liability) carried during the course of construction, with liability limits for death of or injury
to persons and for damages to property in amounts acceptable to Agent or such other limits if any
are established under the construction contract(s). Without limiting the provision in Section 9(D)
herein or the foregoing, the Company agrees to obtain Builder’s Risk casualty insurance covering
fire and other casualty with extended coverage including vandalism and malicious mischief.

(vi) Environmental Audit. A written report of an environmental audit pertaining to the
Company’s real property located near Fairmont, Nebraska, produced by an independent national or
regional environmental consulting firm or such other evidence satisfactory to Agent, which report
or evidence shall show to Agent’s satisfaction that all appropriate inquiry was made and that the
past or present use or condition of the property poses neither material health or safety hazards
nor potential financial exposure that Agent in its sole discretion, finds unacceptable.

(vii) Evidence of Capital. Such evidence as Agent may require that the Company has obtained:
(i) equity capital or acceptable binding commitments thereof (including non-repayable Tax
Increment Financing and grants), in an amount not less than $54,600,000.00 with terms and
conditions acceptable to Agent; and (ii) subordinate Industrial Revenue Bond financing from
Fillmore County, Nebraska, in the amount of $7,000,000.00 exclusive of any related issuance costs
and reserve requirements).

(viii) Process/Yield Guarantee. An acceptable Process/Yield Guarantee from the design engineer
and contractor, acceptable to Agent, as well as a minimum one-year warranty on all work performed.

(ix) Engineering and Construction Contracts. Copies of all engineering and construction
contracts with payment retainages, fixed-priced provisions and warranty provisions acceptable to
Agent.

(x) Utilities; Access. A certificate from the Company’s engineer or other evidence
satisfactory to Agent as to the methods of access to and egress from the Property and the
availability of water supply, electricity, natural gas, and other utilities, and for the disposal
of wastewater, all in locations and capacities sufficient to meet the reasonable requirements of
the Property and the Improvements (as that term is defined in the applicable Supplements) and
otherwise satisfactory to Agent.

(xi) Project Budget and Schedule, Contracts and Plans. Project budget, schedule, contracts and
plans as follows: (i) a budget setting forth the total estimated direct costs for construction
(including real property acquisition, site preparation and infrastructure, railroad siding,
capitalized interest and contingencies) not to exceed an aggregate total of $127,800,000.00 for the
Improvements, and for indirect costs, (including costs to organize and obtain financing, to pay
claims and liabilities, and for pre-production expenses, but excluding working capital) not to
exceed an aggregate total of $5,000,000.00, including line item cost breakdowns for all direct
costs by trade, job, and subcontractor, and a schedule of all sources of funds to pay such costs
(the “Project Budget”); (ii) a schedule setting forth, by trade, job, and subcontractor, the
estimated dates of commencement and completion of construction of the Improvements (the “Project
Schedule”); (iii) a schedule of the amounts and times of advances anticipated to be requisitioned
by the Company from time to time during the term of construction of the Improvements (the
“Disbursement Schedule”); (iv) a list of all subcontractors and materialmen who have been, or, to
the extent then determined by the Company, will be supplying labor, materials or goods for the
Improvements; (v) two sets of the Plans with a certification from the Company and from the
Company’s architect or engineer, or with other evidence satisfactory to Agent as to the following
matters: (a) that the Improvements can be completed by, August 31, 2007, (the “Completion Date”);
(b) that the Project Budget, Project Schedule, Disbursement Schedule and the Plans satisfactorily
provide for the construction of the Improvements; and (c) that the Improvements upon completion
will comply with all Laws (as defined in Section 9(B) hereof), including, without limitation, all
Laws relating to the environment, and all approvals, consents, permits and licenses required under
such Laws (the “Project Approvals”) which have been obtained or are to be obtained by the Company
relating in any way to the acquisition, construction or the contemplated operation of the
Improvements (including, without limitation, those relating to zoning, building, use and occupancy,
fire prevention and health); and (vi) a list of the Project Approvals indicating those Project
Approvals obtained and to be obtained (and a schedule for obtaining such Project Approvals).

(xii) Escrow Agreement. An escrow agreement for distribution of loan funds acceptable to Agent
specifically providing for a Title/Abstract Company to distribute all loan proceeds. Costs of said
agreement are to be paid by the Company.

(xiii) Survey. Receipt of an ALTA quality survey of the Property by a licensed surveyor
satisfactory to Agent verifying no encroachments by any Improvements on the Property onto adjoining
property, or such other information as may be required by Agent.

(xiv) Appraisal. An appraisal of the Property by a licensed, independent appraiser
satisfactory to Agent, such appraisal to include values for the proposed ethanol facility and rail
spur to be located on the Company’s real property located near Fairmont, Nebraska.

(xv) Opinion of Counsel. An opinion of the Company’s counsel (in form and substance acceptable
to Agent) confirming due authorization and execution of all loan, security, and related documents,
and that all loan, security, and related documents constitute binding obligations of the Company
enforceable in accordance with their terms.

(B) Conditions to Each Supplement. Farm Credit’s obligation to extend credit under each
Supplement, including the initial Supplement, is subject to the conditions precedent that Agent
receive, in form and content satisfactory to Agent, each of the following:

(i) Supplement. A duly executed copy of the Supplement and all instruments and documents
contemplated thereby.

(ii) Evidence of Authority. Such certified board resolutions, certificates of incumbency, and
other evidence that Agent may require that the Supplement, all instruments and documents executed
in connection therewith, and, in the case of initial Supplement hereto, this agreement and all
instruments and documents executed in connection herewith, have been duly authorized and executed.

(iii) Fees and Other Charges. All fees and other charges provided for herein or in the
Supplement.

(iv) Evidence of Perfection, Etc. Such evidence as Agent may require that Farm Credit has a
duly perfected first priority lien on all security for the Company’s obligations, and that the
Company is in compliance with Section 9(D) hereof.

(C) Conditions to Each Loan. Farm Credit’s obligation under each Supplement to make any loan
to the Company thereunder is subject to the condition that no “Event of Default” (as defined in
Section 12 hereof) or event which with the giving of notice and/or the passage of time would become
an Event of Default hereunder (a “Potential Default”), shall have occurred and be continuing.

SECTION 8. Representations and Warranties.

(A) This Agreement. The Company represents and warrants to Farm Credit and Agent that as of
the date of this Agreement:

(i) Compliance. The Company and, to the extent contemplated hereunder, each “Subsidiary” (as
defined below), is in compliance with all of the terms of this agreement, and no Event of Default
or Potential Default exists hereunder.

(ii) Subsidiaries. The Company has no Subsidiary(ies) as defined below. For purposes hereof, a
“Subsidiary” shall mean a corporation of which shares of stock having ordinary voting power to
elect a majority of the board of directors or other managers of such corporation are owned,
directly or indirectly, by the Company.

(B) Each Supplement. The execution by the Company of each Supplement hereto shall constitute a
representation and warranty to Agent that:

(i) Applications. Each representation and warranty and all information set forth in any
application or other documents submitted in connection with, or to induce Farm Credit to enter
into, such Supplement, is correct in all material respects as of the date of the Supplement.

(ii) Conflicting Agreements, Etc. This agreement, the Supplements, and all security and other
instruments and documents relating hereto and thereto (collectively, at any time, the “Loan
Documents”), do not conflict with, or require the consent of any party to, any other agreement to
which the Company is a party or by which it or its property may be bound or affected, and do not
conflict with any provision of the Company’s operating agreement, articles of organization, or
other organizational documents.

(iii) Compliance. The Company and, to the extent contemplated hereunder, each Subsidiary, is
in compliance with all of the terms of the Loan Documents (including, without limitation, Section
9(A) of this agreement on eligibility to borrow from Farm Credit).

(iv) Binding Agreement. The Loan Documents create legal, valid, and binding obligations of the
Company which are enforceable in accordance with their terms, except to the extent that enforcement
may be limited by applicable bankruptcy, insolvency, or similar laws affecting creditors’ rights
generally.

SECTION 9. Affirmative Covenants. Unless otherwise agreed to in writing by Agent while this
agreement is in effect, the Company agrees to, and with respect to Subsections 9(B) through 9(G)
hereof, agrees to cause each Subsidiary to:

(A) Eligibility. Maintain its status as an entity eligible to borrow from Farm Credit pursuant
to the terms of the Farm Credit Act of 1971, as amended, 12 USC 2001, et seq.

(B) Company Existence, Licenses, Etc. (i) Preserve and keep in full force and effect its
existence and good standing in the jurisdiction of its formation; (ii) qualify and remain qualified
to transact business in all jurisdictions where such qualification is required; and (iii) obtain
and maintain all licenses, certificates, permits, authorizations, approvals, and the like which are
material to the conduct of its business or required by law, rule, regulation, ordinance, code,
order, and the like (collectively, “Laws”).

(C) Compliance with Laws. Comply in all material respects with all applicable Laws, including,
without limitation, all Laws relating to environmental protection. In addition, the Company agrees
to cause all persons occupying or present on any of its properties, and to cause each Subsidiary to
cause all persons occupying or present on any of its properties, to comply in all material respects
with all environmental protection Laws.

(D) Insurance. Maintain insurance with insurance companies or associations reasonably
acceptable to Agent in such amounts and covering such risks as are usually carried by companies
engaged in the same or similar business and similarly situated, and make such increases in the type
or amount of coverage as Agent may reasonably request. All such policies insuring any collateral
for the Company’s obligations to Farm Credit shall have mortgagee or lender loss payable clauses or
endorsements in form and content acceptable to Agent. At Agent’s request, all policies (or such
other proof of compliance with this Subsection as may be satisfactory to Agent) shall be delivered
to Agent.

(E) Property Maintenance. Maintain all of its property that is necessary to or useful in the
proper conduct of its business in good working condition, ordinary wear and tear excepted.

(F) Books and Records. Keep adequate records and books of account in which complete entries
will be made in accordance with generally accepted accounting principles (“GAAP”) consistently
applied.

(G) Inspection. Permit Agent or its agents, upon reasonable notice and during normal business
hours or at such other times as the parties may agree, to examine its properties, books, and
records, and to discuss its affairs, finances, and accounts, with its respective officers,
directors, employees, and independent certified public accountants.

(H) Reports and Notices. Furnish to Agent:

(i) Annual Financial Statements. As soon as available, but in no event more than 90 days after
the end of each fiscal year of the Company and Advanced BioEnergy, LLC (“Advanced”) occurring
during the term hereof, annual consolidated and consolidating financial statements of the Company
and Advanced, and their consolidated Subsidiaries, if any, prepared in accordance with GAAP
consistently applied. Furthermore, as soon as available, but in no event more than 120 days after
the end of each fiscal year of Advanced occurring during the term hereof, annual unconsolidated
financial statements of Advanced, prepared in accordance with GAAP consistently applied. Such
financial statements shall: (a) be audited by independent certified public accountants selected by
the Company and Advanced and acceptable to Agent; (b) be accompanied by a report of such
accountants containing an opinion thereon acceptable to Agent; (c) be prepared in reasonable detail
and in comparative form; and (d) include a balance sheet, a statement of income, a statement of
retained earnings, a statement of cash flows, and all notes and schedules relating thereto.

(ii) Interim Financial Statements. Effective with the commencement of operations, as soon as
available, but in no event more than 30 days after the end of each month, a consolidated balance
sheet of the Company and its consolidated Subsidiaries, if any, as of the end of such month, a
consolidated statement of income for the Company and its consolidated Subsidiaries, if any for such
period and for the period year to date, and such other interim statements as Agent may reasonably
request, all prepared in reasonable detail and in comparative form in accordance with GAAP
consistently applied and, if required by written notice from Agent, certified by an authorized
officer or employee of the Company acceptable to Agent.

(iii) Notice of Default. Promptly after becoming aware thereof, notice of the occurrence of an
Event of Default or a Potential Default.

(iv) Notice of Non-Environmental Litigation. Promptly after the commencement thereof, notice
of the commencement of all actions, suits, or proceedings before any court, arbitrator, or
governmental department, commission, board, bureau, agency, or instrumentality affecting the
Company or any Subsidiary which, if determined adversely to the Company or any such Subsidiary,
could have a material adverse effect on the financial condition, properties, profits, or operations
of the Company or any such Subsidiary.

(v) Notice of Environmental Litigation, Etc. Promptly after receipt thereof, notice of the
receipt of all pleadings, orders, complaints, indictments, or any other communication alleging a
condition that may require the Company or any Subsidiary to undertake or to contribute to a cleanup
or other response under environmental Laws, or which seek penalties, damages, injunctive relief, or
criminal sanctions related to alleged violations of such Laws, or which claim personal injury or
property damage to any person as a result of environmental factors or conditions.

(vi) Formation Documents. Promptly after any change in the Company’s operating agreement or
articles of organization (or like documents), copies of all such changes, certified by the
Company’s Secretary.

(vii) Budgets. As soon as available, but in no event more than 90 days after the end of any
fiscal year of the Company occurring during the term hereof, copies of the Company’s board-approved
annual budgets and forecasts of operations and capital expenditures.

(viii) Compliance Certificate. Together with each set of financial statements furnished to
Agent pursuant to Subsection (H)(ii) hereof, a certificate of an officer of employee of the Company
acceptable to Agent, in the form attached as Exhibit “A” hereto: (a) certifying that no Event of
Default or Potential Default occurred during the period covered by such statement(s) or, if an
Event of Default or Potential Default occurred, a description thereof and of all actions taken or
to be taken to remedy same, and (b) setting forth calculations showing compliance with the
financial covenants set forth in Section 11 hereof.

(ix) Other Information. Such other information regarding the condition or operations,
financial or otherwise, of the Company or any Subsidiary as Agent may from time to time reasonably
request, including but not limited to copies of all pleadings, notices, and communications referred
to in Subsections 9(H)(iv) and (v) above.

(I) Policies/Contracts. Enter into and provide copies to Agent of each of the following by no
later than January 1, 2007: (i) risk management policies and programs/strategies pertaining to
grain procurement and ethanol and related byproduct marketing; (ii) distillers grain and ethanol
marketing contracts; and (iii) hedging and grain procurement contracts. Furthermore, the Company
agrees to obtain Agent’s written consent prior to making any material changes therein.

(K) Performance Bonds. Provide performance bonds, in form and content acceptable to Agent, for
construction and related contracts upon request by Agent.

SECTION 10. Negative Covenants. Unless otherwise agreed to in writing by Agent, while this
agreement is in effect the Company will not:

(A) Borrowings. Create, incur, assume, or allow to exist, directly or indirectly, any
indebtedness or liability for borrowed money (including trade or bankers’ acceptances), letters of
credit, or the deferred purchase price of property or services, except for: (i) debt to Farm
Credit; (ii) accounts payable to trade creditors incurred in the ordinary course of business; (iii)
current operating liabilities (other than for borrowed money) incurred in the ordinary course of
business (iv) Industrial Revenue Bond financing from Fillmore County, Nebraska, in an amount not to
exceed $7,000,000.00 (exclusive of any related insurance costs and reserve requirements), subject
to a debt subordination agreement acceptable to Agent; and (v) debt of the Company to miscellaneous
creditors, in an aggregate amount not to exceed $1,500,000.00 on terms and conditions satisfactory
to Agent.

(B) Liens. Create, incur, assume, or allow to exist any mortgage, deed of trust, pledge, lien
(including the lien of an attachment, judgment, or execution), security interest, or other
encumbrance of any kind upon any of its property, real or personal (collectively, “Liens”). The
foregoing restrictions shall not apply to: (i) Liens in favor of Farm Credit; (ii) Liens for taxes,
assessments, or governmental charges that are not past due; (iii) Liens and deposits under workers’
compensation, unemployment insurance, and social security Laws; (iv) Liens and deposits to secure
the performance of bids, tenders, contracts (other than contracts for the payment of money), and
like obligations arising in the ordinary course of business, as conducted on the date hereof; (v)
Liens imposed by Law in favor of mechanics, materialmen, warehousemen, and like persons that secure
obligations that are not past due; (vi) easements, rights-ofway, restrictions, and other similar
encumbrances which, in the aggregate, do not materially interfere with the occupation, use, and
enjoyment of the property or assets encumbered thereby in the normal course of its business or
materially impair the value of the property subject thereto; and (vii) subordinate Liens securing
permitted borrowings specified in Sections 10(A)(iv) and 10(A)(v) above.

(C) Mergers, Acquisitions, Etc. Merge or consolidate with any other entity or acquire all or a
material part of the assets of any person or entity, or form or create any new Subsidiary or
affiliate, or commence operations under any other name, organization, or entity, including any
joint venture.

(D) Transfer of Assets. Sell, transfer, lease, or otherwise dispose of any of its assets,
except in the ordinary course of business.

(E) Loans and Investments. Make any loan or advance to any person or entity, or purchase any
capital stock, obligations or other securities of, make any capital contribution to, or otherwise
invest in any person or entity, or form or create any partnerships or joint ventures except trade
credit extended in the ordinary course of business.

(F) Contingent Liabilities. Assume, guarantee, become liable as a surety, endorse,
contingently agree to purchase, or otherwise be or become liable, directly or indirectly
(including, but not limited to, by means of a maintenance agreement, an asset or stock purchase
agreement, or any other agreement designed to ensure any creditor against loss), for or on account
of the obligation of any person or entity, except by the endorsement of negotiable instruments for
deposit or collection or similar transactions in the ordinary course of the Company’s business.

(G) Change in Business. Engage in any business activities or operations substantially
different from or unrelated to the Company’s present business activities or operations.

(H) Capital Expenditures. Beginning with fiscal year ending 2008, expend, in the aggregate,
during any fiscal year more than $600,000.00 for the acquisition of fixed or capital assets
(including all obligations under capitalized leases authorized under the terms of this agreement,
but excluding obligations under operating leases).

(I) Leases. Create, incur, assume, or permit to exist any obligation as lessee under operating
leases or leases which should be capitalized in accordance with GAAP for the rental or hire of any
real or personal property, except for: (i) leases which do not in the aggregate require the Company
to make scheduled payments to the lessors in any fiscal year of the Company in excess of
$100,000.00; and (ii) leases of up to 230 railroad cars with said leases having original maturities
of no more than sixty (60) months under terms and conditions acceptable to Agent.

(J) Changes to Operating Agreements, Etc. Amend or otherwise make any material changes to the
Company’s Articles of Organization, Operating Agreement, management contracts and ethanol and/or
distillers grain marketing contracts.

(K) Dividends, Etc. Declare or pay any dividends, or make any distribution of assets to the
member/owners, or purchase, redeem, retire or otherwise acquire for value any of its equity, or
allocate or otherwise set apart any sum for any of the foregoing, except that for each fiscal year
commencing with the fiscal year ending 2007, a distribution may be made to the Company’s
members/owners of up to 50% of the net profit (according to GAAP) for such fiscal year after
receipt of the audited financial statements for the pertinent fiscal year, provided that the
Company has been and will remain in compliance with all loan covenants, terms and conditions.
Furthermore, with respect to fiscal year ending 2007 and each subsequent fiscal year, a
distribution may be made to its members/owners in excess of 50% of the net profit for such fiscal
year if the Company has made the required “Free Cash Flow” payment to Agent for such fiscal year as
provided in Construction and Term Loan Supplement dated February 17, 2006, and numbered RI0340T01
and any renewals, restatements and amendments thereof, and will remain in compliance with all other
loan covenant, terms and conditions.

(L) Payments on Subordinate Debt. In accordance with, and as permitted by, the terms of the
Debt Subordination Agreement dated as of April 15, 2006, between the Agent, Advanced BioEnergy,
LLC, Wells Fargo Bank, National Association, as trustee, and Farm Credit Services of America, FLCA,
make any payments on the subordinated debt that would cause the Company to be in violation of the
terms of this Agreement.

SECTION 11. Financial Covenants. Unless otherwise agreed to in writing, while this agreement
is in effect:

(A) Working Capital. The Company will have at the end of each period for which financial
statements are required to be furnished pursuant to Section 9(H) hereof, an excess of current
assets over current liabilities (both as determined in accordance with GAAP consistently applied)
of not less than $10,000,000.00 at the earlier of commencement of operations or by September 30,
2007, except that in determining current assets, any amount available under the Construction and
Revolving Term Loan Supplement hereto (less the amount that would be considered a current liability
under GAAP if fully advanced) may be included.

(B) Net Worth. The Company will have at the end of each period for which financial statements
are required to be furnished under Section 9(H) hereof an excess of total assets over total
liabilities (both as determined in accordance with GAAP consistently applied) of not less than: (i)
$50,000,000.00; (ii) increasing to $53,000,000.00 as of March 31, 2008; and (iii) increasing to
$56,000,000.00 at fiscal year ending 2008 and thereafter.

(C) Debt Service Coverage Ratio. The Company will have at the end of each fiscal year of the
Company, effective with the fiscal year ending 2008, a “Debt Service Coverage Ratio” (as defined
below) for that year of not less than 1.25 to 1.00. For purposes hereof, the term “Debt Service
Coverage Ratio” shall mean the following (all as calculated for the most current year-end in
accordance with GAAP consistently applied): (i) net income (after taxes), plus depreciation and
amortization; divided by (ii) all current portion of regularly scheduled long term debt for the
prior period (previous year-end).

SECTION 12. Events of Default. Each of the following shall constitute an “Event of Default”
under this agreement:

(A) Payment Default. The Company should fail to make any payment to Agent, or purchase any
equity in Farm Credit, when due.

(B) Representations and Warranties. Any representation or warranty made or deemed made by the
Company herein or in any Supplement, application, agreement, certificate, or other document related
to or furnished in connection with this agreement or any Supplement, shall prove to have been false
or misleading in any material respect on or as of the date made or deemed made.

(C) Certain Affirmative Covenants. The Company or, to the extent required hereunder, any
Subsidiary should fail to perform or comply with Sections 9(A) through 9(H)(ii), 9(H)(vi) through
9(H)(viii) or any reporting covenant set forth in any Supplement hereto, and such failure continues
for 15 days after written notice thereof shall have been delivered by Agent to the Company.

(D) Other Covenants and Agreements. The Company or, to the extent required hereunder, any
Subsidiary should fail to perform or comply with any other covenant or agreement contained herein
or in any other Loan Document or shall use the proceeds of any loan for an unauthorized purpose.

(E) Cross-Default. The Company should, after any applicable grace period, breach or be in
default under the terms of any other agreement between the Company and Farm Credit.

(F) Other Indebtedness. The Company or any Subsidiary should fail to pay when due any
indebtedness to any other person or entity for borrowed money or any long-term obligation for the
deferred purchase price of property (including any capitalized lease), or any other event occurs
which, under any agreement or instrument relating to such indebtedness or obligation, has the
effect of accelerating or permitting the acceleration of such indebtedness or obligation, whether
or not such indebtedness or obligation is actually accelerated or the right to accelerate is
conditioned on the giving of notice, the passage of time, or otherwise.

(G) Judgments. A judgment, decree, or order for the payment of money shall be rendered against
the Company or any Subsidiary in an amount exceeding $100,000.00 and either: (i) enforcement
proceedings shall have been commenced, (ii) a Lien prohibited under Section 10(B) hereof shall have
been obtained, or (iii) such judgment, decree, or order shall continue unsatisfied and in effect
for a period of 20 consecutive days without being vacated, discharged, satisfied, or stayed pending
appeal.

(H) Insolvency, Etc. The Company or any Subsidiary shall: (i) become insolvent or shall
generally not, or shall be unable to, or shall admit in writing its inability to, pay its debts as
they come due; or (ii) suspend its business operations or a material part thereof or make an
assignment for the benefit of creditors; or (iii) apply for, consent to, or acquiesce in the
appointment of a trustee, receiver, or other custodian for it or any of its property or, in the
absence of such application, consent, or acquiescence, a trustee, receiver, or other custodian is
so appointed; or (iv) commence or have commenced against it any proceeding under any bankruptcy,
reorganization, arrangement, readjustment of debt, dissolution, or liquidation Law of any
jurisdiction.

(I) Material Adverse Change. Any material adverse change occurs, as reasonably determined by
Agent, in the Company’s financial condition, results of operation, or ability to perform its
obligations hereunder or under any instrument or document contemplated hereby.

(J) Revocation of Guaranty. Any guaranty, suretyship, subordination agreement, maintenance
agreement, or other agreement furnished in connection with the Company’s obligations hereunder and
under any Supplement shall, at any time, cease to be in full force and effect, or shall be revoked
or declared null and void, or the validity or enforceability thereof shall be contested by the
guarantor, surety or other maker thereof (the “Guarantor”), or the Guarantor shall deny any further
liability or obligation thereunder, or shall fail to perform its obligations thereunder, or any
representation or warranty set forth therein shall be breached, or the Guarantor shall breach or be
in default under the terms of any other agreement with Agent (including any loan agreement or
security agreement), or a default set forth in Subsections (F) through (H) hereof shall occur with
respect to the Guarantor.

SECTION 13. Remedies. Upon the occurrence and during the continuance of an Event of Default or
any Potential Default, Farm Credit shall have no obligation to continue to extend credit to the
Company and may discontinue doing so at any time without prior notice. For all purposes hereof, the
term “Potential Default” means the occurrence of any event which, with the passage of time or the
giving of notice or both would become an Event of Default. In addition, upon the occurrence and
during the continuance of any Event of Default, Farm Credit or Agent may, upon notice to the
Company, terminate any commitment and declare the entire unpaid principal balance of the loans, all
accrued interest thereon, and all other amounts payable under this agreement, all Supplements, and
the other Loan Documents to be immediately due and payable. Upon such a declaration, the unpaid
principal balance of the loans and all such other amounts shall become immediately due and payable,
without protest, presentment, demand, or further notice of any kind, all of which are hereby
expressly waived by the Company. In addition, upon such an acceleration:

(A) Enforcement. Farm Credit or Agent may proceed to protect, exercise, and enforce such
rights and remedies as may be provided by this agreement, any other Loan Document or under Law.
Each and every one of such rights and remedies shall be cumulative and may be exercised from time
to time, and no failure on the part of Farm Credit or Agent to exercise, and no delay in
exercising, any right or remedy shall operate as a waiver thereof, and no single or partial
exercise of any right or remedy shall preclude any other or future exercise thereof, or the
exercise of any other right. Without limiting the foregoing, Agent may hold and/or set off and
apply against the Company’s obligations to Farm Credit cash collateral held by Farm Credit or
Agent, or any balances held by Farm Credit or Agent for the Company’s account (whether or not such
balances are then due).

(B) Application of Funds. Agent may apply all payments received by it to the Company’s
obligations to Farm Credit in such order and manner as Agent may elect in its sole discretion.

In addition to the rights and remedies set forth above: (i) if the Company fails to purchase any
equity in Farm Credit when required or fails to make any payment to Agent when due, then at Agent’s
option in each instance, such payment shall bear interest from the date due to the date paid at 4%
per annum in excess of the rate(s) of interest that would otherwise be in effect on that loan; and
(ii) after the maturity of any loan (whether as a result of acceleration or otherwise), the unpaid
principal balance of such loan (including without limitation, principal, interest, fees and
expenses) shall automatically bear interest at 4% per annum in excess of the rate(s) of interest
that would otherwise be in effect on that loan. All interest provided for herein shall be payable
on demand and shall be calculated on the basis of a year consisting of 360 days.

SECTION 14. Broken Funding Surcharge. Notwithstanding any provision contained in any
Supplement giving the Company the right to repay any loan prior to the date it would otherwise be
due and payable, the Company agrees to provide three Business Days’ prior written notice for any
prepayment of a fixed rate balance and that in the event it repays any fixed rate balance prior to
its scheduled due date or prior to the last day of the fixed rate period applicable thereto
(whether such payment is made voluntarily, as a result of an acceleration, or otherwise), the
Company will pay to Agent a surcharge in an amount equal to the greater of: (i) an amount which
would result in Farm Credit, Agent, and all subparticipants being made whole (on a present value
basis) for the actual or imputed funding losses incurred by Farm Credit, Agent, and all
subparticipants as a result thereof; or (ii) $300.00. Notwithstanding the foregoing, in the event
any fixed rate balance is repaid as a result of the Company refinancing the loan with another
lender or by other means, then in lieu of the foregoing, the Company shall pay to Agent a surcharge
in an amount sufficient (on a present value basis) to enable Farm Credit, Agent, and all
subparticipants to maintain the yield they would have earned during the fixed rate period on the
amount repaid. Such surcharges will be calculated in accordance with methodology established by
Farm Credit, Agent, and all subparticipants (copies of which will be made available to the Company
upon request).

SECTION 15. Complete Agreement, Amendments. This agreement, all Supplements, and all other
instruments and documents contemplated hereby and thereby, are intended by the parties to be a
complete and final expression of their agreement. No amendment or modification of this Agreement
shall be effective unless in writing signed by both parties hereto. No waiver of any provision
hereof, and no consent to any departure by either party herefrom, shall be effective unless
approved in writing by the other party, and then such waiver or consent shall be effective only in
the specific instance and for the specific purpose for which given. In the event this agreement is
amended or restated, each such amendment or restatement shall be applicable to all Supplements
hereto.

SECTION 16. Other Types of Credit. From time to time, Farm Credit may extend other types of
credit to or for the account of the Company to expedite or facilitate the loans extended hereunder.
In the event the parties desire to do so under the terms of this agreement, such extensions of
credit may be set forth in any Supplement hereto and this agreement shall be applicable thereto.

SECTION 17. Applicable Law. Except to the extent governed by applicable federal law, this
agreement and each Supplement shall be governed by and construed in accordance with the laws of the
State of Colorado, without reference to choice of law doctrine.

SECTION 18. Notices. All notices hereunder shall be in writing and shall be deemed to be duly
given upon delivery if personally delivered or sent by telegram or facsimile transmission, or three
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):

If to Agent, as follows:

For general correspondence purposes: CoBank, ACB

P.O. Box 5110

Denver, Colorado 80217-5110

For direct delivery purposes, when desired: CoBank, ACB

5500 South Quebec Street

Greenwood Village, Colorado 80111-1914

Attention: Credit Information Services

Fax No.: (303) 224-6101

If to the Company, as follows:

ABE Fairmont, LLC

137 North 8th Street Geneva, Nebraska 68361

Attention: Revis Stephenson III

Fax No.: (402) 759-3774

SECTION 19. Taxes and Expenses. To the extent allowed by law, the Company agrees to pay all
reasonable out-of-pocket costs and expenses (including the fees and expenses of counsel retained or
employed by Agent, including expenses of in-house counsel of Agent) incurred by Agent and any
participants from Farm Credit in connection with the origination, administration, collection, and
enforcement of this agreement and the other Loan Documents, including, without limitation, all
costs and expenses incurred in perfecting, maintaining, determining the priority of, and releasing
any security for the Company’s obligations to Farm Credit, and any stamp, intangible, transfer, or
like tax payable in connection with this agreement or any other Loan Document.

SECTION 20. Effectiveness and Severability. This agreement shall continue in effect until: (i)
all indebtedness and obligations of the Company under this agreement, all Supplements, and all
other Loan Documents shall have been paid or satisfied; (ii) Agent has no commitment to extend
credit to or for the account of the Company under any Supplement; and (iii) either party sends
written notice to the other terminating this agreement. Any provision of this agreement or any
other Loan Document which is prohibited or unenforceable in any jurisdiction shall, as to such
jurisdiction, be ineffective to the extent of such prohibition or unenforceability without
invalidating the remaining provisions hereof or thereof.

SECTION 21. Successors and Assigns. This agreement, each Supplement, and the other Loan
Documents shall be binding upon and inure to the benefit of the Company and Farm Credit and their
respective successors and assigns, except that the Company may not assign or transfer its rights or
obligations under this agreement, any Supplement or any other Loan Document without the prior
written consent of Agent.

SECTION 22. Participations, Etc. From time to time, Farm Credit may sell to one or more banks,
financial institutions or other lenders a participation in one or more of the loans or other
extensions of credit made pursuant to this agreement. However, no such participation shall relieve
Farm Credit of any commitment made to the Company under any Supplement hereto. In connection with
the foregoing, Farm Credit may disclose information concerning the Company and its Subsidiaries to
any participant or prospective participant, provided that such participant or prospective
participant agrees to keep such information confidential. Farm Credit agrees that all Loans that
are made by Farm Credit and that are retained for its own account and are not included in a sale of
participation interest shall be entitled to patronage distributions in accordance with the bylaws
of Farm Credit and its practices and procedures related to patronage distribution. Accordingly, all
Loans that are included in a sale of participation interest shall not be entitled to patronage
distributions from Farm Credit. A sale of participation interest may include certain voting rights
of the participants regarding the loans hereunder (including without limitation the administration,
servicing and enforcement thereof). Farm Credit agrees to give written notification to the Company
of any sale of participation interests.

SECTION 23. Counterparts. This agreement, each Supplement and any other Loan Document may be
executed in any number of counterparts and by different parties hereto in separate counterparts,
each of which, when so executed, shall be deemed to be an original and shall be binding upon all
parties and their respective permitted successors and assigns, and all of which taken together
shall constitute one and the same agreement.

SECTION 24. Administrative Fee. The Company agrees to pay to Agent on November 1, 2007, and on
each November 1 thereafter, for as long as the Company has commitments from Farm Credit, an
administrative fee in the amount of $35,000.00.

SECTION 25. Assumed Master Loan Agreement. The parties acknowledge that the Company has
assumed the Master Loan Agreement dated as of February 17, 2006, between Farm Credit and Advanced
BioEnergy, LLC, as the same may have been amended from time to time (the “Advanced MLA”), together
with all obligations thereunder and under all Supplements, security documents, and other documents
related thereto. The parties agree that the Advanced MLA shall remain in full force and effect
concurrently with this MLA, provided, however, that to the extent of any inconsistencies between
this MLA and the Advanced MLA, the terms and conditions of this MLA (including without reporting
covenants, financial covenants, and negative and affirmative covenants) shall prevail, and the
Advanced MLA shall be deemed amended accordingly. Consistently with the foregoing, all Conditions
Precedent to lending under this MLA shall apply to, and be binding upon, any lending under the
Advanced MLA.

IN WITNESS WHEREOF, the parties have caused this agreement 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
	
 
	 	 
	
 
	 	11/27/06

1

	 	 	EXHIBIT A

FARM CREDIT SERVICES OF AMERICA, FLCA

COMPLIANCE CERTIFICATE

This certificate is being furnished to CoBANK, ACB (“CoBank”), as agent for Farm Credit
Services of America, FLCA (“Farm Credit”) to induce CoBank to make and/or continue to make advances
to the Company and to comply with and demonstrate compliance with the terms, covenants, and
conditions of the Company’s Master Loan Agreement and all Supplements thereto. The undersigned
hereby certifies that: (i) this certificate was prepared from the books and records of the Company,
is in agreement with them, and is correct to the best of the undersigned’s knowledge and belief;
(ii) no “Event of Default” (as defined in the Master Loan Agreement) or event which, with the
giving of notice and/or the passage of time and/or the occurrence of any other condition, would
ripen into an Event of Default (a “Potential Default”) shall have occurred and be continuing,
except as disclosed below; and (iii) based upon the undersigned’s review of the attached financial
statement(s) dated as of      , to the best of the undersigned’s knowledge, the
attached financial statement(s) are accurate and complete for the period reflected. Each of the
following Financial Covenants shall have the meanings ascribed thereto in Section 11 of the
Company’s Master Loan Agreement.

This certificate is attached to and made a part of the Company’s financial statements for the
reporting period ending .

	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	TARGET RESULT	 	 	 	 
	FINANCIAL COVENANT	 	REQUIRED	 	CALCULATION(S)	 	ACTUAL
	 	 	 	 	 	 	Monthly beginning the	 	 
	 	 	 	 	 	 	earlier of commencement	 	 
	 	 	 	 	 	 	of operations or	 	 
	Working Capital	 	$10,000,000.00	 	9/30/07	 	$_______________
	 
	 	$	50,000,000.00	 	 	Monthly	 	 	 	 
	 
	 	$	53,000,000.00	 	 	Monthly starting 03/31/08	 	 	 	 
	Net Worth
	 	$	56,000,000.00	 	 	Monthly starting FYE 2008	 	$	_______________	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 
	Debt Service
	 	 	 	 	 	Fiscal Year End starting	 	 	 	 
	Coverage Ratio
	 	 	1.25 : 1.00	 	 	FYE 2008	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 

OTHER COMMENTS, INCLUDING A DESCRIPTION OF ANY DEFAULTS AND CORRECTIVE ACTIONS BEING UNDERTAKEN:

ABE FAIRMONT, LLC

By: ADVANCED BIOENERGY, LLC, its sole member

Authorized Signature

2EX-10.2

EXHIBIT 10.2

CONSTRUCTION AND TERM LOAN SUPPLEMENT

THIS SUPPLEMENT to the Master Loan Agreement dated November 20, 2006, (the “MLA”), 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”).

SECTION 1. The Construction and Term Loan Commitment. On the terms and conditions set forth in
the MLA and this Supplement, Farm Credit agrees to make construction loans to the Company from time
to time during the period set forth below in an aggregate principal amount not to exceed, at any
one time outstanding, $6,500,000.00 (the “Commitment”). Under the Commitment, amounts borrowed and
later repaid may not be reborrowed. No advance shall be made until evidence has been provided to
the Agent (as that term is defined in the MLA) as required in Section 7(A)(vii) of the MLA that all
requisite equity funds have been received by the Company and that such funds shall have been
utilized for the construction of the Improvements (as defined herein).

SECTION 2. Purpose. The purpose of the Commitment is to partially finance the Company’s
construction of a 100 million gallon (annual) ethanol plant (the “Improvements”) identified in the
plans and specifications provided to and approved by Agent pursuant to Section 7(A)(xi) of the MLA
(as the same may be amended pursuant to Section 12(A) herein, the “Plans”), on real property owned
by the Company near Fairmont, Nebraska (the “Property”), and the Company agrees to utilize the
proceeds of the Commitment for that purpose only.

SECTION 3. Term. The term of the Commitment shall be from the date hereof, up to and including
September 1, 2007, or such later date as Agent may, in its sole discretion, authorize in writing.

SECTION 4. Disbursements of Proceeds.

(A) Disbursement Procedures.

(1) Limits on Advances. Agent shall not be required to advance funds: (i) for any category or
line item of acquisition or construction cost an amount greater than the amount specified therefor
in the Project Budget (as defined in Section 7(A)(xi) of the MLA); or (ii) for any services not yet
performed or for materials or goods not yet incorporated into the Improvements or delivered to and
properly stored on the Property. No advance hereunder shall exceed 100% of the aggregate costs
actually paid or currently due and payable and represented by invoices accompanying a Request for
Construction Loan Advance submitted pursuant to Section 9(B)(1) herein less the amount of retainage
(“Retainage”) set out in the construction contract between the Company and Fagen, Inc., and other
construction contracts of the Company for the Improvements.

(2) Advance of Retainage. The Retainage (but in no case greater than the unused balance of the
Commitment allocated for construction) will be advanced by Agent to the Company pursuant to the
conditions set forth in such construction contracts, upon written request by the Company certifying
the satisfaction of such conditions precedent for payment of Retainage.

(B) Payments to Third Parties. If there is an Event of Default (as defined in the MLA) at its
option and without further authorization from the Company, Agent is authorized to make advances
under the Commitment by paying, directly or jointly with the Company, any person to whom Agent in

1

good faith determines payment is due and any such advance shall be deemed made as of the
date on which Agent makes such payment and shall be secured under the deed of trust/mortgage
securing the Commitment and any other loan documents securing the Commitment as fully as if made
directly to the Company.

SECTION 5. Interest and Fees.

(A) Interest. The Company agrees to pay interest on the unpaid principal balance of the loans
in accordance with one or more of the following interest rate options, as selected by the Company:

(1) Agent Base Rate. At a rate per annum equal at all times to 50 Basis Points above the rate
of interest established by Agent from time to time as its Agent Base Rate, which Rate is intended
by Agent to be a reference rate and not its lowest rate. The Agent Base Rate will change on the
date established by Agent as the effective date of any change therein and Agent agrees to notify
the Company of any such change.

(2) Quoted Rate. At a fixed rate per annum to be quoted by Agent in its sole discretion in
each instance. Under this option, rates may be fixed on such balances and for such periods, as may
be agreeable to Agent in its sole discretion in each instance, provided that: (1) the minimum fixed
period shall be 180 days; (2) amounts may be fixed in increments of $500,000.00 or multiples
thereof; and (3) the maximum number of fixes in place at any one time shall be ten.

(3) LIBOR. At a fixed rate per annum equal to “LIBOR” (as hereinafter defined) plus 3.40%.
Under this option: (1) rates may be fixed for “Interest Periods” (as hereinafter defined) of 1, 2,
3, 6, 9, or 12 months as selected by the Company; (2) amounts may be fixed in increments of
$500,000.00 or multiples thereof; (3) the maximum number of fixes in place at any one time shall be
ten; and (4) rates may only be fixed on a “Banking Day” (as hereinafter defined) on 3 Banking Days’
prior written notice. For purposes hereof: (a) “LIBOR” shall mean the rate (rounded upward to the
nearest sixteenth and adjusted for reserves required on “Eurocurrency Liabilities” (as hereinafter
defined) for banks subject to “FRB Regulation D” (as herein defined) or required by any other
federal law or regulation) quoted by the British Bankers Association (the “BBA”) at 11:00 a.m.
London time 2 Banking Days before the commencement of the Interest Period for the offering of U.S.
dollar deposits in the London interbank market for the Interest Period designated by the Company;
as published by Bloomberg or another major information vendor listed on BBA’s official website; (b)
“Banking Day” shall mean a day on which Agent is open for business, dealings in U.S. dollar
deposits are being carried out in the London interbank market, and banks are open for business in
New York City and London, England; (c) “Interest Period” shall mean a period commencing on the date
this option is to take effect and ending on the numerically corresponding day in the next calendar
month or the month that is 2, 3, 6, 9, or 12 months thereafter, as the case may be; provided,
however, that: (i) in the event such ending day is not a Banking Day, such period shall be extended
to the next Banking Day unless such next Banking Day falls in the next calendar month, in which
case it shall end on the preceding Banking Day; and (ii) if there is no numerically corresponding
day in the month, then such period shall end on the last Banking Day in the relevant month; (d)
“Eurocurrency Liabilities” shall have meaning as set forth in “FRB Regulation D”; and (e) “FRB
Regulation D” shall mean Regulation D as promulgated by the Board of Governors of the Federal
Reserve System, 12 CFR Part 204, as amended.

2

The Company shall select the applicable rate option at the time it requests a loan hereunder
and may, subject to the limitations set forth above, elect to convert balances bearing interest at
the variable rate option to one of the fixed rate options. Upon the expiration of any fixed rate
period, interest shall automatically accrue at the variable rate option unless the amount fixed is
repaid or fixed for an additional period in accordance with the terms hereof. Notwithstanding the
foregoing, rates may not be fixed in such a manner as to cause the Company to have to break any
fixed rate balance in order to pay any installment of principal. All elections provided for herein
shall be made electronically (if applicable), telephonically or in writing and must be received by
Agent not later than 12:00 Noon Company’s local time in order to be considered to have been
received on that day; provided, however, that in the case of LIBOR rate loans, all such elections
must be confirmed in writing upon Agent’s request. Interest shall be calculated on the actual
number of days each loan is outstanding on the basis of a year consisting of 360 days and shall be
payable monthly in arrears by the 20th day of the following month or on such other day in such
month as Agent shall require in a written notice to the Company; provided, however, in the event
the Company elects to fix all or a portion of the indebtedness outstanding under the LIBOR interest
rate option above, at Agent’s option upon written notice to the Company, interest shall be payable
at the maturity of the Interest Period and if the LIBOR interest rate fix is for a period longer
than 3 months, interest on that portion of the indebtedness outstanding shall be payable quarterly
in arrears on each three-month anniversary of the commencement date of such Interest Period, and at
maturity.

(B) Loan Origination Fee. In consideration of the Commitment, the Company agrees to pay to
Agent a loan origination fee in the amount of $72,500.00 (less any payments already received by
Agent) upon the execution hereof.

SECTION 6. Promissory Note. The Company promises to repay the loans on June 1, 2009. 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.

SECTION 7. Prepayment. Subject to the broken funding surcharge provision of the MLA, the
Company may on one Business Day’s prior written notice prepay all or any portion of the loan(s).
Unless otherwise agreed, all prepayments will be applied to principal installments in the inverse
order of their maturity. However, in addition to the foregoing, prepayment of any Loan balance due
to refinancing, or refinancing of any unadvanced Commitment, up to and including June 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.

SECTION 8. Security. Security is set forth in the MLA.
SECTION 9. Additional Conditions Precedent.

(A) Initial Advance. Agent’s obligation to make the initial advance is subject to the
satisfaction of each of the following additional conditions precedent on or before the date of such
advance:

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(1) List of Permits. Receipt by Agent of a detailed list of all permits required for
both the construction of the improvements and the operation of the facility setting forth for each
listed permit whether such permit is required for commencement of construction or required for
commencement of operation, and identifying to Agent’s satisfaction whether such permits have been
issued or can reasonably be expected to be issued.

(2) Construction Permits. Receipt by Agent of evidence of issuance of all permits that are
required to be obtained prior to the commencement of construction of the improvements.

(3) Engineer’s Certificate. Receipt by Agent of a report of Agent’s retained engineer
(pursuant to the provisions of Section 14(D)) indicating that the current plans and specifications
of the Improvements and the related contracts establish that the finished project will have
adequate natural gas, electricity, water and waste water treatment to service the requirements of
the project.

(B) Each Advance. Agent’s obligation to make each advance hereunder, including the initial
advance, is subject to the satisfaction of each of the following additional conditions precedent on
or before the date of such advance:

(1) Request for Construction Loan Advance. That Agent receives an executed request for
construction loan advance from the Company in the form of Exhibit A attached hereto (the “Request
for Construction Loan Advance”), together with all items called for therein.

(2) Construction Certificate. If an independent inspector has been employed by Agent pursuant
to Section 14(D), a certificate or report of such inspector to the effect that the construction of
the Improvements to the date thereof has been performed in a good and workmanlike manner and in
accordance with the Plans, stating the estimated total cost of construction of the Improvements,
stating the percentage of in-place construction of the Improvements, and stating that the remaining
non-disbursed portion of the Commitment is adequate to complete the construction of the
Improvements.

SECTION 10. Representations and Warranties. In addition to the representations and warranties
contained in the MLA, the Company represents and warrants as follows:

(A) Project Approvals; Consents; Compliance. The Company has obtained all Project Approvals
relating to the construction and operation of the Improvements, except those the Company has
disclosed to Agent in writing. All such Project Approvals heretofore obtained remain in full force
and effect and the Company has no reason to believe that any such Project Approval not heretofore
obtained will not be obtained by the Company in the ordinary course during or following completion
of the construction of the Improvements. To the extent that any Project Approval may terminate or
become void or voidable or terminable, upon any sale, transfer or other disposition of the Property
or the Improvements, including any transfer pursuant to foreclosure sale under the Mortgage, the
Company will cooperate with Agent to obtain any replacement Project Approvals. No consent,
permission, authorization, order, or license of any governmental authority is necessary in
connection with the execution, delivery, performance, or enforcement of the loan documents to which
the Company is a party, except such as have been obtained and are in full force and effect. The
Company is in compliance in all material respects with all Project Approvals having application to
the Property or the Improvements except as the Company has disclosed to Agent in writing. Without
limiting the foregoing, there are no

4

unpaid or outstanding real estate or other taxes or assessments on or against the Property
or the Improvements or any part thereof (except only real estate taxes not yet due and payable).
The Company has received no notice nor has any knowledge of any pending or contemplated assessments
against the Property or the Improvements which have not been disclosed to Agent in writing.

(B) Environmental Compliance. Without limiting the provisions of the MLA, all property owned
or leased by the Company, including, without limitation, the Property and the Improvements, and all
operations conducted by it are in compliance in all material respects with all Laws and all Project
Approvals relating to environmental protection, the failure to comply with which could have a
material adverse effect on the condition, financial or otherwise, operations, properties, or
business of the Company, or on the ability of the Company to perform its obligations under the loan
documents, except as the Company has disclosed to Agent in writing.

(C) Feasibility. Each of the Project Budget, the Project Schedule and the Disbursement
Schedule is realistic and feasible.

SECTION 11. Affirmative Covenants. In addition to the affirmative covenants contained in the
MLA, the Company agrees to:

(A) Reports and Notices. Furnish to Agent:

(1) Regulatory and Other Notices. Promptly after receipt thereof, copies of any notices or
other communications received from any governmental authority with respect to the Property, the
Improvements, or any matter or proceeding the effect of which could have a material adverse effect
on the condition, financial or otherwise, operations, properties, or business of the Company, or
the ability of the Company to perform its obligations under the loan documents.

(2) Notice of Nonpayment. Promptly after the filing or receipt thereof, a description of or a
copy of any lien filed by or any notice, whether oral or written, from any laborer, contractor,
subcontractor or materialman to the effect that such laborer, contractor, subcontractor or
materialman has not been paid when due for any labor or materials furnished in connection with the
construction of the Improvements.

(3) Notice of Suspension of Work. Prompt notice of any suspension in the construction of the
Improvements, regardless of the cause thereof, in excess of ten (10) days and a description of the
cause for such suspension.

(B) Construction Liens. Pay or cause to be removed, within fifteen (15) days after notice from
Agent, any lien on the Improvements or Property, provided, however, that Company shall have the
right to contest in good faith and with reasonable diligence the validity of any such lien or
claim.

(C) Identity of Contractors, etc. Furnish to Agent from time to time on request by Agent, in a
form acceptable to Agent, correct lists of all contractors, subcontractors and suppliers of labor
and material supplied in connection with construction of the Improvements and true and correct
copies of all executed contracts, subcontracts and supply contracts. Agent may contact any
contractor, subcontractor or supplier to verify any facts disclosed in the lists and contracts. All
contracts and subcontracts relating

5

to construction of the Improvements must contain provisions authorizing or not prohibiting
the Company to supply to Agent the listed information and copies of contracts or not otherwise
prohibiting any transfers.

(D) Lien Waivers. Furnish to Agent, at any time and from time to time upon the request of
Agent, lien waivers bearing a then current date and prepared on a form satisfactory to Agent from
such contractor, subcontractor, or supplier as Agent shall designate.

(E) Operating Permits. Furnish to Agent, unless as otherwise consented to in writing by Agent,
as soon as possible but prior to the commencement of operation of the constructed facility,
evidence of the issuance of all necessary permits for such operation.

SECTION 12. Negative Covenants. In addition to the negative covenants contained in the MLA,
the Company will not:

(A) Change Orders. Allow any substantial deviation, addition, extra, or change order to the
Plans, Project Budget or Project Schedule, the cost of which in the aggregate exceeds $100,000.00,
without Agent’s prior written approval. All requests for substantial changes shall be made using a
Change Order Request in the form of Exhibit B attached hereto. Agent will have a reasonable time to
evaluate any requests for its approval of any changes referred to in this covenant, and will not be
required to consider approving any changes unless all other approvals that may be required have
been obtained. Agent may approve or disapprove changes in its discretion. All contracts and
subcontracts relating to the construction of the Improvements must contain provisions satisfactory
to Agent implementing the above provisions of this covenant. Company shall promptly provide to
Agent copies of all change orders that, pursuant to the above described procedures, did not require
Agent’s prior written approval.

(B) Materials. Purchase or install any materials, equipment, fixtures or articles of personal
property for the Improvements if such shall be covered under any security agreement or other
agreement where the seller reserves or purports to reserve title or the right of removal or
repossession, or the right to consider them personal property after their incorporation in the
Improvements.

SECTION 13. Casualties.

(A) Right to Elect to Apply Proceeds. In case of material loss or damage to the Property or to
the Improvements by fire, by a taking by condemnation for public use or the action of any
governmental authority or agency, or the transfer by private sale in lieu thereof, either
temporarily or permanently, or otherwise, if in the sole judgment of Agent there is reasonable
doubt as to Company’s ability to complete construction of the Improvements on or before August 31,
2007, by reason of such loss or damage or because of delays in making settlements with governmental
agencies or authorities or with insurers, Agent may terminate its obligations to make advances
hereunder and elect to collect, retain and apply to the Commitment all proceeds of the taking or
insurance after deduction of all expense of collection and settlement, including attorneys’ and
adjusters’ fees and charges. In the event such proceeds are insufficient to pay the Commitment in
full, Agent may declare the balance remaining unpaid on the Commitment to be due and payable
forthwith and avail itself on any of the remedies afforded thereby as in any case of default.

6

(B) Election Not to Apply Proceeds. In case Agent does not elect to apply such proceeds
to the Commitment, Company will:

(1) Settle. Proceed with diligence to make settlement with the governmental agencies or
authorities or the insurers and cause the proceeds of insurance to be paid to Company.

(2) Resume Construction. Promptly proceed with the resumption of construction of the
Improvements, including the repair of all damage resulting from such fire or other cause and
restoration to its former condition.

(C) Use of Proceeds. All such proceeds shall be fully used before the disbursement of any
further proceeds of the Commitment.

SECTION 14. Other Rights of Agent.

(A) Right to Inspect. Agent or its agent may enter on the Property at any time and inspect the
Improvements. If the construction of the Improvements is not reasonably satisfactory to Agent,
Agent may reasonably and in good faith stop the construction and order its replacement or the
correction thereof or additions thereto, whether or not said unsatisfactory construction has been
incorporated in the Improvements, and withhold all advances hereunder until such construction is
satisfactory to Agent. Such construction shall promptly be made satisfactory to Agent.

(B) Obligation of Agent. Neither Agent nor any inspector hired pursuant to Subsection (D)
below is obligated to construct or supervise construction of the Improvements. Inspection by Agent
or such inspector thereof is for the sole purpose of protecting Agent’s security and is not to be
construed as a representation that there will be compliance on anyone’s part with the Plans or that
the construction will be free from faulty material or workmanship. Neither Agent nor such inspector
shall be liable to the Company or any other person concerning the quality of construction of the
Improvements or the absence therefrom of defects. The Company will make or cause to be made such
other independent inspections as it may desire for its own protection.

(C) Right to Complete Upon Event of Default. Upon any Event of Default hereunder, Agent may
complete construction of the Improvements, subject to Agent’s right at any time to discontinue any
work without liability, and apply the proceeds of the Commitment to such completion, and may demand
such additional sums from the Company as may be necessary to complete construction, which sums the
Company shall promptly pay to Agent. In connection with any construction of the Improvements
undertaken by Agent pursuant to this Subsection, Agent may (i) enter upon the Property; (ii) employ
existing contractors, architects, engineers and subcontractors or terminate them and employ others;
(iii) make such addition, changes and corrections in the Plans as shall, in the judgment of Agent,
be necessary or desirable; (iv) take over and use any personal property, materials, fixtures,
machinery, or equipment of the Company to be incorporated into or used in connection with the
construction or operation of the Improvements; (v) pay, settle, or compromise all existing or
future bills and claims which are or may be liens against the Property or the Improvements; and
(vi) take such other action, as Agent may in its sole discretion determine, to complete the
construction of the Improvements. The Company shall be liable to Agent for all costs paid or
incurred for construction of the Improvements, and all payments made hereunder shall be deemed
advances by Agent, shall be evidenced by the Note and shall

7

be secured by the Mortgage and any other loan document securing the Commitment (including
any amounts in excess of the Commitment).

(D) Right to Employ Independent Engineer. Agent reserves the right to employ an independent
construction engineer, among other things, to review the Project Budget, the Project Schedule and
the Plans, inspect all construction of the Improvements and the periodic progress of the same, and
review all Draw Requests and change orders, the cost therefor to be the sole responsibility of the
Company and shall be paid by the Company upon demand by Agent.

(E) Indemnification and Hold Harmless. The Company shall indemnify and hold Farm Credit and
Agent harmless from and against all liability, cost or damage arising out of this Agreement or any
other loan document or the transactions contemplated hereby and thereby, including, without
limitation, (i) any alleged or actual violation of any Law or Project Approval relating to the
Property or the Improvements and (ii) any condition of the Property or the Improvements whether
relating to the quality of construction or otherwise and whether Agent elects to complete
construction upon an Event of Default or discontinues or suspends construction pursuant to this
Section 14. Agent may commence, appear in or defend any such action or proceeding or any other
action or proceeding purporting to affect the rights, duties or liabilities of the parties
hereunder, or the Improvements, or the Property, or the payment of the Commitment, and the Company
agrees to pay all of Agent’s costs and expenses, including its reasonable attorneys’ fees, in any
such actions. The obligations of the Company under this Subsection 14(E) shall survive the
termination of this Agreement. As to any action or inaction taken by Agent hereunder, Agent shall
not be liable for any error of judgment or mistake of fact or law, absent gross negligence or
willful misconduct on its part. The Company’s obligation to indemnify and hold Agent harmless
hereunder will exclude any liability, cost, or damage related to Agent’s breach of this Agreement
or for Agent’s gross negligence or willful misconduct.

SECTION 15. Notice of Completion. Company irrevocably appoints Agent as Company’s agent to
file of record any notice of completion, cessation of labor or any other notice that Agent deems
necessary to file to protect any of the interests of Agent. Agent, however, shall have no duty to
make such filing.

SECTION 16. Signs and Publicity. At Farm Credit’s and Agent’s request, Company will allow Farm
Credit and Agent to post signs on the Property at the construction site for the purpose of
identifying Farm Credit and Agent as the “Construction Lenders”. At the request of Farm Credit and
Agent, Company will use its best efforts to identify Farm Credit and Agent as the construction
lenders in publicity concerning the project.

SECTION 17. Cooperation. Company will cooperate at all times with Agent in bringing about the
timely completion of the Improvements, and Company will resolve all disputes arising during the
work of construction in a manner which will allow work to proceed expeditiously.

SECTION 18. Events of Default. In addition to the events of default set forth in the MLA, each
of the following shall constitute an “Event of Default” hereunder:

(A) Cessation of Construction. Any cessation at any time in the construction of the
Improvements for more than thirty (30) consecutive days, except for strikes, acts of God, or other
causes

beyond the Company’s control, or any cessation at any time in construction of the
Improvements for more than thirty (30) consecutive days, regardless of the cause.

(B) Insufficiency of Loan Proceeds. Agent, in its sole discretion shall determine that the
remaining undisbursed portion of the Commitment is or will be insufficient to fully complete the
Improvements in accordance with the Plans.

SECTION 19. Remedies Upon Default. In addition to the remedies set forth in the MLA, upon the
occurrence of and during the continuance of each and every Event of Default Agent may (but shall
not be obligated to) take over and complete construction of the Improvements in accordance with
plans and specifications approved by Agent with such changes as Agent may, in its sole discretion,
deem appropriate, all at the risk, cost, and expense of the Company. Agent may assume or reject any
contracts entered into by the Company in connection with the Improvements, and may enter into
additional or different contracts for services, labor, and materials required, in the judgment of
Agent, to complete the construction of the Improvements and may pay, compromise, and settle all
claims in connection with the construction of the Improvements. All sums, including reasonable
attorneys’ fees, charges, or fees for supervision and inspection of the construction, and for any
other necessary purpose in the discretion of Agent, expended by Agent in completing the
construction of the Improvements (whether aggregating more or less than the amount of this
Commitment) shall be deemed advances made by Agent to the Company under this Commitment, and the
Company shall be liable to Agent for the repayment of such sums, together with interest on such
amounts from the date of their expenditure at the default rate specified above. Agent may, in its
sole discretion, at any time, abandon work on the construction of the Improvements after having
commenced such work, and may recommence such work at any time, it being understood that nothing in
this Section shall impose any obligation on Agent to either complete or not to complete the
construction of the Improvements. For the purposes of carrying out the provisions of this Section,
the Company irrevocably appoints Agent, its attorney-in-fact, with full power of substitution, to
execute and deliver all such documents, pay and receive such funds, and take such action as may be
necessary, in the judgment of Agent, to complete the construction of the Improvements.

IN WITNESS WHEREOF, the parties have caused this Supplement 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

11/27/06

8

EXHIBIT A

REQUEST FOR LOAN ADVANCE

	 	 	 	 	 
	Request No.

	 	 	 	Date:
	 
	 	 	 	 
	 
	 	 
	 
	 	 	 	 
	To:

From:

	 	CoBank, ACB

ABE Fairmont, LLC
	 	

	
 
	 	 
	 	 
	
 
	 	(Name of Borrower)

Loan Agreement No. RI0475T01
	 	

Dated: November 20, 2006
	
 
	 	 
	 	 
	
 
	 	Project Description:
	 	

	
 
	 	 
	 	 
	
 
	 	Project Location:
	 	

	
 
	 	 
	 	 

In accordance with the terms of the above referenced Loan Agreement, you are hereby authorized and
requested to make a construction advance, as set forth in said Loan Agreement, of the amount and
for the items set forth in the request schedule attached hereto as Schedule “A” and incorporated
herein.

The undersigned hereby certify that:

	1.	 	The labor, services and/or materials covered hereby have been performed upon or furnished to
the above referenced project and are accurately described in the supporting invoices attached
to the request schedule;

	2.	 	There have been no changes in the cost breakdown for the project dated      
supplied to Agent, except those approved in writing by Agent.

	3.	 	All construction to date has been substantially performed in accordance with the Plans for
the Improvements, and there have been no changes in the Plans except as approved in writing by
Agent;

	4.	 	There have been no material changes in the scope or time of performance of the work of
construction, nor any extra work, labor or materials ordered or contracted for, nor are any
such changes or extras contemplated, except as may be expressly permitted by the Loan
Agreement or as have been approved in writing by Agent;

	5.	 	The payments to be made with the requested funds will pay all bills received to date, less
any required withholds, for labor, materials, equipment and/or services furnished in
connection with the construction of the Improvements; and

	6.	 	All amounts previously advanced by Agent for labor, services, equipment and/or materials for
the above referenced project pursuant to previous Requests for Construction Loan Disbursement
have been paid to the parties entitled thereto in the manner required in the Loan Agreement.

9

	7.	 	All conditions to the advance of Loan funds required herein as set forth in the Loan
Agreement have been fulfilled, and to the actual knowledge of the undersigned, no Event of
Default under the Loan Agreement has occurred and is continuing.

BORROWER:

ABE FAIRMONT, LLC

By ADVANCED BIOENERGY, LLC, its sole member

By:

ENGINEER:

By:

CONTRACTOR:

FAGEN, INC.

By:

We have reviewed the Pay Application Numbered and dated . Based on our conversations with the
Contractor and the Owner, our review of the current schedule, and our site observations, the
construction in place is judged to be in general accordance with industry standards and in general
conformity with the approved plans and specifications, proceeding generally on schedule, and the
request for payment is a reasonable representation of the materials ordered and the work effort of
the Contractor to date.

AGENT’S CONSULTING ENGINEER:

By:

APPROVED FOR PAYMENT BY AGENT: CoBANK,

ACB

By:

Date:

10

EXHIBIT B

CHANGE ORDER REQUEST

	 	 	 	 	 
	Date:_______________	 	 
	Request No. CO#	 	 
	To:	 	CoBank, ACB	 	 
	From:	 	ABE Fairmont, LLC	 	 
	 	 	(Name of Borrower)	 	 
	
 
	 	Loan Agreement No. RI0475T01
	 	Dated: November 20, 2006
	
 
	 	 
	 	 
	
 
	 	Project Description:
	 	

	
 
	 	 
	 	 
	
 
	 	Project Location:
	 	

	
 
	 	 
	 	 

In accordance with the terms of the above referenced Loan Agreement, the undersigned hereby
requests that Agent approve the change orders more particularly described in the schedule attached
hereto as Schedule “A” and incorporated herein.

The undersigned hereby certifies that:

	1.	 	There have been no changes in the Plans and or contracts except those permitted in the Loan
Agreement and/or approved in writing by Agent; and

	2.	 	Copies of the proposed changes to the Plans and/or contracts are attached hereto as Schedule
“B” and that all such documents are complete and fully comply with all applicable permits and
approvals, subject to the written approval of Agent.

BORROWER: ENGINEER: ABE FAIRMONT, LLC

	 	 	 
	By ADVANCED BIOENERGY, LLC, its sole member
	By:

	 	By:
	CONTRACTOR:

	 	

	FAGEN, INC.

	 	

	 

	 	

	By:

	 	

	 

	 	

CHANGE ORDER APPROVED BY AGENT:
CoBANK, ACB

By:

Date:

11

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