STOCKHOLDERS AGREEMENT

Exhibit 10.6

STOCKHOLDERS AGREEMENT

     THIS STOCKHOLDERS AGREEMENT (the “ Agreement ”) is made as of the 3rd day of July, 2008 (the “ Effective Date ”), by and between Alon USA Energy, Inc., a Delaware corporation (“ Alon USA ”), Alon Refining Louisiana, Inc., a Delaware corporation (the “ Company ”), Alon Louisiana Holdings, Inc., a Delaware corporation (“ Alon LA ”), Alon Israel Oil Company, Ltd., an Israeli limited liability company (“ Alon Israel ” and, together with Alon LA, the “ Stockholders ”), and any other stockholder who from time to time becomes party to this Agreement by execution of a joinder agreement in form and substance reasonably acceptable to the Stockholders.

RECITALS :

     A. On the date hereof, Alon Israel is purchasing 80,000 shares of the Company’s Series A Preferred Stock, par value $1,000.00 per share (the “ Preferred Stock ”), pursuant to that certain Series A Stock Purchase Agreement dated as of the date hereof by and between the Company and Alon Israel (the “ Purchase Agreement ”);

     B. The Purchase Agreement contemplates that this Agreement be executed by the parties hereto on even date therewith, and the parties are willing to execute this Agreement and be bound by the provisions hereof; and

     C. The parties hereto desire to agree upon the terms on which the securities of the Company, now or hereafter outstanding and held by them, will be held and transferred.

AGREEMENT :

     NOW, THEREFORE, in consideration of the foregoing and the mutual covenants and agreements hereinafter set forth, the parties hereto agree as follows:

1. Definitions .

     1.1 Certain Interpretive Matters . When a reference is made in this Agreement to Sections, such reference will be to a Section of this Agreement unless otherwise indicated. Whenever the words “include,” “includes” or “including” are used in this Agreement, they will be deemed to be followed by the words “without limitation.” Unless the context otherwise requires, (i) “or” is disjunctive but not necessarily exclusive, (ii) words in the singular include the plural and vice versa, (iii) the use in this Agreement of a pronoun in reference to a party hereto includes the masculine, feminine or neuter, as the context may require, (iv) the use in this Agreement of “day” will mean a calendar day unless indicated otherwise, (v) all references to $ or dollar amounts will be to lawful currency of the United States, and (vi) the words “herein”, “hereby”, “hereof”, and “hereunder” and other words of similar import refer to this Agreement as a whole and not to any particular section, paragraph or other subdivision of this Agreement.

     1.2 Number of Shares of Stock . Whenever any provision of this Agreement calls for any calculation based on a number of shares of capital stock issued and outstanding or held by a Stockholder, the number of shares deemed to be issued and outstanding or held by that Stockholder, unless specifically stated otherwise, as applicable, shall be the total number of

shares of the Company’s Common Stock, par value $0.01 per share (the “ Common Stock ”), or Preferred Stock then issued and outstanding or owned by such Stockholder, as applicable.

     1.3 Defined Terms . The following capitalized terms, as used in this Agreement, shall have the meanings set forth below.

     “ Affiliate ” shall mean with respect to any Person (as defined below), any Person who, directly or indirectly, controls, is controlled by or is under common control with such Person, including any partner, officer, director, member, manager or employee of such Person.

     “ Change of Control ” means either of the following events:

     (a) the failure, for any reason, of Alon USA to beneficially own, directly or indirectly, at least a majority of the voting stock of the Company or, if applicable, any entity that succeeds to all or substantially all of the assets of the Company by purchase, contribution, assignment, merger, consolidation or otherwise; or

     (a) the failure, for any reason, of Alon Israel to beneficially own, directly or indirectly, at least a majority of the voting stock of Alon USA or, if applicable, any entity that succeeds to all or substantially all of the assets of Alon USA by purchase, contribution, assignment, merger, consolidation or otherwise.

     “ Alon Common Stock ” shall mean the shares of common stock, par value $0.01 per share, of Alon USA Energy, Inc., a Delaware corporation.

     “ Alon Share Price ” shall mean the greater of (i) the average of the daily closing sales prices per share of the Alon Common Stock on the New York Stock Exchange for each trading day during the period commencing on the day 90 days prior to the date of this Agreement and (ii) the closing sale price per share of the Alon Common Stock on the New York Stock Exchange on the date of this Agreement.

     “ Business Day ” means a day other than a Saturday, Sunday or other day on which commercial banks in Dallas, Texas are not open for business.

     “ Certificate ” means the Company’s Amended and Restated Certificate of Incorporation, as in effect from time to time.

     “ Par Value ” means $1,000 per share of Series A Preferred Stock.

     “ Permitted Transferee ” means any Person to which a Stockholder may Transfer Securities as permitted by and in accordance with Sections 2.1 and 2.2 of this Agreement.

     “ Person ” means an individual, a corporation, an association, a joint venture, a partnership, a limited liability company, an estate, a trust, an unincorporated organization and any other entity or organization, governmental or otherwise.

     “ Securities ” means, at any time, any shares of capital stock of the Company, including Common Stock and Preferred Stock now or hereafter issued by the Company, together with any

options thereon and any other shares of stock directly or indirectly issued or issuable with respect thereto, whether by way of a stock dividend, stock split or in exchange for or upon conversion of such shares or otherwise in connection with a combination of shares, recapitalization, merger, consolidation or other corporate reorganization, and any instrument convertible into or exercisable or exchangeable for (in each case, directly or indirectly) shares of capital stock of the Company, together with any shares of stock issued or issuable with respect thereto.

     “ Securities Act ” means the Securities Act of 1933, as amended, and the rules and regulations promulgated thereunder.

     “ Series A Dividends ” has the meaning set forth in the Certificate.

     “ Share Exchange ” means the issuance and delivery by Alon USA to Alon Israel and/or any of its Permitted Transferees in exchange for all of the shares of Preferred Stock then held by Alon Israel and/or any of its Permitted Transferees a number of duly authorized, fully paid and nonassessable whole shares of Alon Common Stock as determined in accordance with Section 2.3(c) hereof.

     “ Transfer ” means any direct transfer, donation, sale, assignment, pledge, hypothecation, grant of a security interest in or other disposal or attempted disposal of all or any portion of a Security, any interest or rights in a Security, or any rights under this Agreement. “ Transferred ” means the accomplishment of a Transfer, and “ Transferee ” means the recipient of a Transfer.

2. Restrictions on Transfer .

     2.1 Restrictions on Transfer . Each Stockholder agrees that such Stockholder will not, without the prior written consent of the Company, not to be unreasonably withheld, Transfer all or any portion of the Securities now owned or hereafter acquired by such Stockholder, except in connection with, and strictly in compliance with this Article 2. Notwithstanding the foregoing, a Transfer by a Stockholder to any Affiliate of such Stockholder shall not be subject to the prior consent of the Company.

     2.2 Permitted Transfers . Notwithstanding the provisions of Section 2.1, no Transfer shall be permitted or effected hereunder unless and until the Transferee shall have entered into a joinder agreement in form and substance reasonably acceptable to the Stockholders providing that all Securities so Transferred shall continue to be subject to all provisions of this Agreement as if such Securities were still held by such Stockholder (“ Joinder Agreement ”). Notwithstanding anything to the contrary in this Agreement or any failure by a Transferee under this Section 2.2 to execute a Joinder Agreement, such Transferee shall take any Securities so Transferred subject to all provisions of this Agreement as if such Securities were still held by the Stockholder making such Transfer, whether or not they so agree in writing.

     2.3 Exchange Right .

          (a) Subject to the prior receipt by Alon USA of approval of holders of a majority of the Alon Common Stock with respect to the issuance of the Exchange Shares (as defined below) pursuant to and in compliance with Section 312.03 of the NYSE’s Listed Company Manual (“ NYSE Stockholder Approval ”), prior to the consummation of a Change of

Control (a “ Change of Control Date ”), each of Alon USA and Alon Israel shall have the option, exercisable at each such party’s sole and absolute discretion, to require the other party to consummate the Share Exchange by delivery to the other party at least 10 Business Days prior to the Change of Control Date of a written notice (the “ Exercise Notice ”) setting forth such party’s election to effectuate the Share Exchange. Any Share Exchange elected pursuant to this Section 2.3(a) shall be consummated effective as of the Business Day immediately preceding the Change of Control Date (the “ Change of Control Exchange Date ”).

          (b) If a Share Exchange effected pursuant to Section 2.3(a) shall not have occurred prior to 5:00 p.m. (Dallas, Texas time) on July 1, 2011 (the “ Mandatory Exchange Date ”), then, subject to the prior receipt by Alon USA of NYSE Stockholder Approval, Alon USA and Alon Israel and/or any of its Permitted Transferees shall consummate the Share Exchange effective as of the Mandatory Exchange Date.

          (c) Alon USA acknowledges and agrees that it shall include the NYSE Stockholder Approval (and all required disclosures) as a matter to be voted upon in its proxy statement relating to its 2009 annual meeting of stockholders.

          (d) On the Change of Control Exchange Date or Mandatory Exchange Date, as applicable, Alon USA shall issue and deliver to Alon Israel and/or any of its Permitted Transferees in exchange for all of the shares of Preferred Stock then held by Alon Israel and/or any of its Permitted Transferees (all of which shares shall be transferred and delivered to Alon USA free and clear of any lien, claim, judgment, charge, mortgage, security interest, escrow, equity or other encumbrance), a number of duly authorized, fully paid and nonassessable whole shares of Alon Common Stock equal to the quotient obtained by dividing (i) the sum of (A) the aggregate Par Value of the shares of Preferred Stock then held by Alon Israel and/or any of its Permitted Transferees, and (B) the aggregate Series A Dividends accrued but unpaid on such shares of Preferred Stock, whether or not declared, together with any other dividends declared but unpaid on such shares of Preferred Stock, by (ii) the Alon Share Price (the “ Exchange Shares ”); provided that in lieu of any fractional share of Alon Common Stock that would otherwise by payable by operation of this subsection, Alon USA shall pay to the Person entitled ther