Re: Limited Consent and Waiver and Amendment under the Credit Agreement and Account Agreement (each as defined below)

Waiver Agreement

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BIOFUEL ENERGY CORP.

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Title: Re: Limited Consent and Waiver and Amendment under the Credit Agreement and Account Agreement (each as defined below)
Governing Law: New York Date: 5/28/2009
Industry: Chemical Manufacturing Sector: Basic Materials

Re: Limited Consent and Waiver and Amendment under the Credit Agreement and Account Agreement (each as defined below), Parties: biofuel energy corp.

Exhibit 10.1

May 28, 2009

BNP Paribas, as Lender and Administrative Agent

787 Seventh Avenue

New York, NY 10019

Deutsche Bank Trust Company Americas, as Collateral Agent and Depositary Agent

60 Wall Street, 27th Floor

Mail Stop: NYC60-2710

New York, NY 10005

The Lender parties to the Credit

Agreement (as defined below)

Re: Limited Consent and Waiver and Amendment under the Credit Agreement and Account Agreement (each as defined below)

Ladies and Gentlemen:

1. This request for limited consent and waiver and amendment (this “ Consent ”) is delivered to you pursuant to (i) that certain Credit Agreement, dated as of September 25, 2006 (as amended, supplemented and modified from time to time, the “ Credit Agreement ”), among BFE Operating Company, LLC (“ Opco ”), Buffalo Lake Energy, LLC (“ Buffalo Lake ”), Pioneer Trail Energy, LLC (“ Pioneer Trail ” and, together with Opco and Buffalo Lake, the “ Borrowers ”), Opco, as Borrowers’ Agent (the “ Borrowers’ Agent ”), the Lenders party thereto, BNP Paribas, as Administrative Agent and Arranger, and Deutsche Bank Trust Company Americas, as Collateral Agent and (ii) that certain Collateral Account Agreement, dated as of September 25, 2006 (as amended, supplemented and modified from time to time, the “ Account Agreement ”), among Borrowers, the Borrowers’ Agent, the Collateral Agent, and Deutsche Bank Trust Company Americas, as the Depositary Agent (the “ Depositary Agent ”). All capitalized terms used herein and not otherwise defined shall have the meanings assigned to such terms in the Credit Agreement.

2. The Borrowers hereby acknowledge having received notice by letter dated May 22, 2009 that: (a) a number of Defaults and Events of Default under the Credit Agreement have occurred and are continuing as of the date hereof; and (b) as a result thereof, the Borrowers cannot satisfy the conditions precedent to borrow funds under the Credit Agreement.

3. Section 6.1(a) of the Account Agreement provides that, on and after the date on which the Depositary Agent has received a notice of an Event of Default (and this Consent constitutes such a notice of an Event of Default pursuant to paragraph 9 of this Consent), the Depositary Agent shall accept all notices and instructions required to be given to the Depositary Agent pursuant to the Account Agreement only from the Collateral Agent (acting on the instructions of the Administrative Agent pursuant to the Credit Agreement) and not from any other Person, and the Depositary Agent shall not withdraw, dispose of, transfer, pay or otherwise distribute any monies in any of the Accounts except pursuant to notices and instructions from the

Collateral Agent (acting on the instructions of the Administrative Agent pursuant to the Credit Agreement).

4. The Borrowers are in immediate need of funds for the purposes and in the amounts specified in Exhibit A and therefore hereby request the Lenders to permit the transfers set forth in paragraph 5 below.

5. Notwithstanding anything to the contrary contained in Section 6.1(c) or any other provision of the Account Agreement but subject to the proviso below in this paragraph, the Collateral Agent (acting on the instructions of the Administrative Agent) hereby instructs the Depositary Agent to not withdraw, dispose of, transfer, pay or otherwise distribute any monies in any of the Accounts except pursuant to Sections 4.2(a)(iv), 4.2(a)(v)(A), 4.2(b), 4.2(d), 4.2(e), 4.3(b), 4.4 and 4.5 of the Account Agreement in accordance with a certificate provided in conformity with the requirements of the Account Agreement for such purpose, unless the Depositary Agent shall have been instructed otherwise in writing by the Collateral Agent (acting on the instructions of the Administrative Agent), in the order of priority set forth in such Sections; provided , however , that the Depository Agent may only make transfers out of the Payment Accounts pursuant to Section 4.3(b) from funds on deposit in the Payment Accounts on the date hereof and solely for the uses and in the amounts specified in Exhibit A . The foregoing consent and waiver shall expire on May 31, 2009 unless otherwise extended by a written consent of the Required Lenders or terminated earlier by a written notice from the Administrative Agent.

6. Exhibit B hereto sets forth the current balances in each of the Accounts as of the date hereof.

7. The parties hereto agree that Section 4.2(b) of the Account Agreement is hereby amended by replacing “Section 4.

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