Document:

exv10w46

Exhibit 10.46

MANAGEMENT EMPLOYMENT AGREEMENT

     This Agreement is entered into between Paul Eisman (“Manager”) and Alon USA GP, LLC, a
Delaware limited liability company (“Employer” or “Company”) on March 1, 2010, who, in return for
the mutual promises set forth herein, agree as follows:

     1. Position/Term. (a) The term of the Manager’s employment hereunder shall be deemed to
have commenced as of March 1, 2010.

          (b) Throughout the term of this Agreement, Employer shall employ Manager and Manager shall
render services to Employer in the capacity and with the title of President of Alon USA Energy,
Inc., or such other title as may be established by Employer from time to time. Manager shall devote
his full time and best effort to the successful functioning of the business of Employer and shall
faithfully and industriously perform all duties pertaining to his position, including such
additional duties as may be assigned from time to time, to the best of Manager’s ability,
experience and talent. Manager shall be subject at all times during the term hereof to the
direction and control of Employer in respect of the work to be done.

          (c) Manager’s employment hereunder shall be for an initial term of five years. Thereafter,
the term shall renew automatically each year for a term of one year, unless either party provides
the other with written notice at least 30 days prior to the expiration of the term.

     2. Compensation. (a) Manager’s salary (“Base Compensation”) shall be $400,000 per
year, payable bi-weekly (unless the payroll practice of the Company changes to monthly or
semi-monthly) in arrears and subject to change only with the mutual written consent of Employer and
Manager. It is the intent of the Company to develop guidelines for annual merit increases for
salaries of all salaried employees/management, including Manager.

          (b) Manager shall be entitled to participate in the Alon USA Annual Cash Bonus Plan which will
be subject to modification in the sole discretion of the Company without advanced notice from time
to time as set forth therein. For purposes of determining the Manager’s Target Bonus Amount under
such plan, the Manager shall participate up to an amount equal to one-hundred percent (100%) of
base compensation.

          (c) Subject to the approval of the stockholders of Alon USA Energy, Inc. at its next annual
meeting of stockholders, Manager shall be granted 500,000 shares of restricted common stock of Alon
USA Energy, Inc., all of which shares shall vest upon the fifth anniversary of the date of grant,
subject to acceleration in certain circumstances. The grant will be subject to the execution by
Manager and Alon USA Energy, Inc. of a grant agreement in substantially the form executed by other
senior executives of the Company.

     3. Fringe Benefits; Reimbursement of Expenses. Employer shall make available, or cause to be
made available to Manager, throughout the period of his employment hereunder, such benefits,
including any disability, hospitalization, medical benefits, life insurance, pension plan or other
benefits or policy, as may be put into effect from time to time by Employer generally for other
Management members at the level of Management. The Company expressly reserves the right to modify
such benefits at any time.

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     Manager will be reimbursed for all reasonable out-of-pocket business, business entertainment
and travel expenses paid by the Manager, in accordance with and subject to applicable Company
expense incurrence and reimbursement policies. Any expense reimbursements required to be made
under this Agreement will be for expenses incurred by Manager during the term of this Agreement,
and such reimbursements will be made not later than December 31st of the year following
the year in which Manager incurs the expense; provided, that in no event will the amount of
expenses eligible for payment or reimbursement in one calendar year affect the amount of expenses
to be paid or reimbursed in any other calendar year. Manager’s right to expense reimbursement will
not be subject to liquidation or exchange for another benefit.

     4. Vacation. The number of vacation days to which Manager shall be entitled each year shall
be based on the years of service of the Manager for Employer as follows — 15 days up to 10 years,
20 days after 10 years, 25 days after 20 years and 30 days after 30 years. Unless otherwise
agreed, vacation may not be carried over into a new calendar year. Vacation time shall be taken
only after providing reasonable notice to the person to whom the Manager reports.

     5. Compliance With Employer Policies. Manager shall comply with and abide by all employment
policies and directives of Employer. Employer may, in its sole discretion, change, modify or adopt
new policies and directives affecting Manager’s employment. In the event of any conflict between
the terms of this Agreement and Employer’s employment policies and directives, the terms of this
Agreement will be controlling.

     6. Restrictive Covenant. In consideration of the confidential business information that
Employer promises to provide Manager access or exposure to during the term of employment as
described in paragraph 7 of the Agreement, Manager agrees to the restrictive covenants set forth in
this paragraph 6 and its subparts:

          (a) Manager agrees that during the term of Manager’s employment with Employer and for a period
of one year following any termination of Manager’s employment, if the Manager terminates employment
during the first two years of Manager’s employment, or nine months, if the Manager terminates
employment after the first two years of employment and before the completion of five years of
employment (the “Non-Compete Period”), Manager will not, without the prior written consent of
Employer, directly or indirectly, either as an individual or as an employee, officer, director,
shareholder, partner, sole proprietor, independent contractor, consultant or in any other capacity
conduct any business, or assist any person in conducting any business, that is in competition with
the business of Employer or its Affiliates (as defined below).

          (b) In addition to any other covenants or agreements to which Manager may be subject, during
the Non-Compete Period, Manager will not, directly or indirectly, either as an individual or as an
employee, officer, director, shareholder, partner, sole proprietor, independent contractor,
consultant or in any other capacity whatsoever approach or solicit any customer or vendor of
Employer with whom the Manager had contact or received information about during the course of
employment for the purpose of causing, directly or indirectly, any such customer or vendor to cease
doing business with Employer or its Affiliates.

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     For the purposes of this Agreement, the “business of Employer or its Affiliates” means the
business of refining petroleum distillates and the wholesale distribution of such products in the
Territory. The term “Affiliates” means all subsidiaries of Employer and each person or entity that
controls, is controlled by, or is under common control with Employer. The “Territory” means the
states of Texas, New Mexico, Arizona, California, Oregon, Washington and Nevada. It is understood
and agreed that the scope of each of the covenants contained in this Section 6 is reasonable as to
time, area, and persons and is necessary to protect the legitimate business interest of Employer.
It is further agreed that such covenants will be regarded as divisible and will be operative as to
time, area and persons to the extent that they may be so operative. The terms of this Section 6
shall not apply to the ownership by Manager of less than 5% of a class of equity securities of an
entity, which securities are publicly traded on the New York Stock Exchange, the American Stock
Exchange, or the National Market System of the National Association of Securities Dealers Automated
Quotation System. The provisions of this Section 6 will survive any termination or expiration of
this Agreement.

     7. Confidentiality. (a) During the course of employment, Employer promises to provide
Manager with access or exposure to information or ideas of a confidential or proprietary nature
which pertain to an area of Employer’s business, financial, legal, marketing, administrative,
personnel, technical or other functions or which constitute trade secrets (including, but not
limited to, as examples specifications, designs, plans, drawings, software, data, prototypes, the
identity of sources and markets, marketing information and strategies; business and financial plans
and strategies, methods of doing business; data processing and management information and technical
systems, programs and practices; customers and users and their needs, sales history; and financial
strength), and such information of third parties which has been provided to Employer in confidence
(“Confidential Information”). All such information is deemed “confidential” or “proprietary”
whether or not it is so marked, provided that it is maintained as confidential by the Company.
Information will not be considered to be Confidential Information to the extent that it is
generally available to the public. Nothing in this Section 7 will prohibit the use or disclosure
by Manager of knowledge that is in general use in the industry or general business knowledge.

          (b) Manager shall hold Confidential Information in confidence, use it only in connection with
the performance of duties on behalf of Employer, and restrict its disclosure to those directors,
employees or independent contractors of Employer having a need to know.

          (c) Manager shall not disclose, copy or use Confidential Information for the benefit of anyone
other than Employer without Employer’s prior written consent.

          (d) Manager shall, upon Employer’s request or Manager’s termination of employment, return to
Employer any and all written documents containing Confidential Information in Manager’s possession,
custody or control.

     8. Non-Interference with Employment Relationships. In consideration of the confidential
business information that Employer promises to provide Manager access or exposure to during the
term of employment as described in paragraph 7 of this Agreement, Manager promises that during the
term of his/her employment with Employer, and for a period of one (1) year thereafter, Manager
shall not, without Employer’s prior written consent, directly or indirectly: (a) induce or attempt
to induce any employee to leave the Employer’s employ; or

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(b) interfere with or disrupt the Employer’s relationship with any of its employees or
independent contractors.

     9. Copyright, Inventions, Patents. Employer shall have all right, title and interest to all
features (including, but not limited to, graphic designs, copyrights, trademarks and patents)
created during the course of or resulting from Manager’s employment with Employer. Manager hereby
assigns to Employer all copyright ownership and rights to any work developed by Manager and reduced
to practice for or on behalf of Employer or which relate to Employer’s business during the course
of the employment relationship. At Employer’s expense, Manager shall do all other things
including, but not limited to, the giving of evidence in suits and proceedings, and the furnishing
and/or assigning of all documentation and other materials relative to Employer’s intellectual
property rights, necessary or appropriate for Employer to obtain, maintain, and assert its rights
in such work.

     10. Termination of Employment. (a) Employer may terminate Manager’s employment hereunder
at any time for Cause. For purposes hereof, Cause shall mean: (i) conviction of a felony or a
misdemeanor where imprisonment is imposed for more than 30 days; (ii) commission of any act of
theft, fraud, dishonesty, or falsification of any employment or Employer records; (iii) improper
disclosure of Confidential Information; (iv) any intentional action by the Manager having a
material detrimental effect on the Company’s reputation or business; (v) any material breach of
this Agreement, which breach is not cured within ten (10) business days following receipt by
Manager of written notice of such breach; (vi) unlawful appropriation of a corporate opportunity;
or (vii) intentional misconduct in connection with the performance of any of Manager’s duties,
including, without limitation, misappropriation of funds or property of the Company, securing or
attempting to secure to the detriment of the Company any profit in connection with any transaction
entered into on behalf of the Company, any material misrepresentation to the Company, or any
knowing violation of law or regulations to which the Company is subject. Upon termination of
Manager’s employment with the Company for Cause, the Company shall be under no further obligation
to Manager, except to pay all earned but unpaid Base Compensation and all accrued benefits and
vacation to the date of termination (and to the extent required by law).

          (b) Employer may terminate Manager’s employment hereunder without Cause, or Manager may
terminate his employment hereunder for Good Reason, upon not less than thirty (30) days prior
written notice. In the event of any such termination, Manager shall be entitled to receive his
Base Compensation through the termination date and any annual bonus entitlement, prorated for the
number of months of employment for the fiscal year in question, all accrued benefits and vacation
to the date of termination (and to the extent required by law), plus, during the first two years
of Manager’s employment hereunder, an amount of severance payment equal to one year’s Base
Compensation as in effect immediately before any notice of termination, or, after the first two
years of Manager’s employment hereunder, an amount of severance payment equal to nine months’ Base
Compensation as in effect immediately before any notice of termination. “Good Reason” means (i)
without the Manager’s prior written consent, the Employer reduces Manager’s Base Compensation or
the percentage of Manager’s Base Compensation established as Manager’s maximum target bonus
percentage for purposes of Employer’s annual cash bonus plan., (ii) any material breach of this
Agreement, which breach is not cured within ten (10) business days following receipt by Employer of
written notice of such

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breach; and (iii) the delivery by Employer of notice pursuant to Section 1 (c) of this
Agreement that it does not wish this Agreement to automatically renew for any subsequent year.

          (c) Manager may terminate the employment relationship hereunder with not less than thirty (30)
days prior written notice. Upon any such termination of Manager’s employment, other than for Good
Reason, the Company shall be under no further obligation to Manager, except to pay all earned but
unpaid Base Compensation and all accrued benefits and vacation to the date of termination (and to
the extent required by law).

          (d) To the extent that a payment becomes due to Manager under this Section 10 by reason of
Manager’s termination of employment, (i) the term “termination of employment” will have the same
meaning as “separation from service” under Section 409A of the Internal Revenue Code of 1986, as
amended (the “Code”), and (ii) except as provided in Section 10(e) below, all such payments will be
made in a single lump sum no later than 60 days after the date on which Manager terminates
employment.

          (e) If the Company makes a good faith determination that a payment under this Agreement (i)
constitutes a deferral of compensation for purposes of Section 409A of the Code, (ii) is made to
Manager by reason of his separation from service and (iii) at the time such payment would otherwise
be made Manager is a “specified employee” as hereinafter defined, the payment will be delayed until
the first day of the seventh month following the date of such termination of employment and will
bear interest at the prime rate of interest as published in the Wall Street Journal on the first
business day following the date of Manager’s termination of employment. For purposes of this
Section 10, a specified employee is an officer of Alon USA Energy, Inc. with annual compensation in
excess of $150,000 (as adjusted for years after 2008), provided that only the 50 highest paid
officers of Alon USA Energy, Inc. may constitute “specified employees” for any 12-month period. An
individual who is identified as a one of the 50 highest paid officers during any portion of a
calendar year will be a specified employee for purposes of the Agreement during the 12-month period
beginning on April 1 of the following calendar year.

          (f) The provisions of Sections 6, 7, 8 and 9 of this Agreement will continue in
effect notwithstanding any termination of Manager’s employment.

     11. Mediation and Arbitration. (a) Employer and Manager hereby state their mutual desire
for any dispute concerning a legally cognizable claim arising out of this Agreement or in
connection with the employment of Manager by Employer, including, but not limited to, claims of
breach of contract, fraud, unlawful termination, discrimination, harassment, workers’ compensation
retaliation, defamation, tortious infliction of emotional distress, unfair competition, and
conversion (“Legal Dispute”), to be resolved amicably, if possible, and without the need for
litigation.

          (b) Based on this mutual desire, in the event a Legal Dispute arises, the parties shall
utilize the following protocol:

               (i) The parties shall first submit the Legal Dispute to mediation under the auspices of the
American Arbitration Association (“AAA”) and pursuant to the mediation rules and procedures
promulgated by the AAA.

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               (ii) In the event mediation is unsuccessful in fully resolving the Legal Dispute, binding
arbitration shall be the method of final resolution of the Legal Dispute. The parties expressly
waive their rights to bring action against one another in a court of law, except as expressly
provided in subsection (d). The parties hereto acknowledge that failure to comply with this
provision shall entitle the non-breaching party not only to damages, but also to injunctive relief
to enjoin the actions of the breaching party. Any Legal Dispute submitted to Arbitration shall be
under the auspices of the AAA and pursuant to the “National Rules for the Resolution of Employment
Disputes,” or any similar identified rules promulgated at such time the Legal Dispute is submitted
for resolution. All mediation and arbitration hearings shall take place in Dallas, Texas.

          (c) Notice of submission of any Legal Dispute to mediation shall be provided no later than
three hundred sixty-five (365) calendar days following the date the submitting party became aware
of the conduct constituting the alleged claims. Failure to do so shall result in the irrevocable
waiver of the claim made in the Legal Dispute.

          (d) Notwithstanding that mediation and arbitration are established as the exclusive procedures
for resolution of any Legal Dispute, (i) either party may apply to an appropriate judicial or
administrative forum for injunctive relief and (ii) claims by Employer arising in connection with
paragraphs 6, 7, 8 or 9 may be brought in any court of competent jurisdiction.

          (e) Each party acknowledges that a remedy at law for any breach or attempted breach of
paragraphs 6, 7, 8 or 9 of this Agreement will be inadequate, agrees that Employer will be entitled
to specific performance and injunctive and other equitable relief in case of any breach or
attempted breach, and agrees not to use as a defense that any party has an adequate remedy at law.
This Agreement shall be enforceable in a court of equity, or other tribunal with jurisdiction, by a
decree of specific performance, and appropriate injunctive relief may be applied for and granted in
connection herewith. Such remedy shall not be exclusive and shall be in addition to any other
remedies now or hereafter existing at law or in equity, by statute or otherwise. Except as
provided in subsection (c) no delay or omission in exercising any right or remedy set forth in this
Agreement shall operate as a waiver thereof or of any other right or remedy and no single or
partial exercise thereof shall preclude any other or further exercise thereof or the exercise of
any other right or remedy.

     12. Assignment. This Agreement shall not be assignable by either party except that upon any
sale or transfer of all or substantially all of its business by Employer, Employer may assign this
Agreement to its successor; any failure to make such an assignment will be considered to constitute
the termination of Manager’s employment without cause effective upon the closing of the referenced
transaction.

     13. No Inducement, Agreement Voluntary. Manager represents that (a) he has not been
pressured, misled, or induced to enter into this Agreement based upon any representation by
Employer or its agents not contained herein, (b) he has entered into this Agreement voluntarily,
after having the opportunity to consult with representatives of his own choosing and that (c) his
agreement is freely given.

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     14. Interpretation and Severability. Any paragraph, phrase or other provision of this
Agreement that is determined by a court, arbitrator or arbitration panel of competent jurisdiction
to be unreasonable or in conflict with any applicable statute or rule, shall be deemed, if
possible, to be modified or altered so that it is not unreasonable or in conflict or, if that is
not possible, then it shall be deemed omitted from this Agreement. The invalidity of any portion
of this Agreement shall not affect the validity of the remaining portions. Further, should any
clause, sentence, provision, paragraph, or part of this Agreement be adjudged by any court of
competent jurisdiction, or be held by any other competent governmental authority having
jurisdiction, to be illegal, invalid, or unenforceable, such judgment or holding shall not affect,
impair, or invalidate the remainder of the Agreement, but shall be confined to the greatest extent
possible in its operation to the particular clause, sentence, provision, paragraph, or part of the
agreement directly involved, and the remainder of the Agreement shall remain in full force and
effect.

     15. Prior Agreements Superseded; Amendments. This Agreement revokes and supersedes all prior
agreements, written and oral, and represents the entire agreement between the parties in relation
to the employment of the Manager by the Company after the Commencement Date and, except as provided
in Section 16 below, shall not be subject to modification or amendment by any oral representation,
or any written statement by either party, except for a dated writing signed by the Manager and the
Employer.

     16. Section 409A of the Code. To the extent that any payment made under this Agreement
constitutes a deferral of compensation subject to Section 409A of the Code, the time of such
payment may not be accelerated except to the extent permitted by Section 409A of the Code. Where
Section 409A of the Code permits a payment or benefit that constitutes a deferral of compensation
to be accelerated, the payment or benefit may be accelerated in the sole discretion of the Company.
Notwithstanding any provision of this Agreement to the contrary, in light of the uncertainty with
respect to the proper application of Section 409A of the Code, the Company reserves the right to
make amendments to this Agreement as the Company deems necessary or desirable solely to avoid the
imposition of taxes or penalties under Section 409A of the Code.

     17. Notices. All notices, demands and requests of any kind to be delivered in connection with
this Agreement shall be in writing and shall be deemed to have been duly given if personally
delivered or if sent by nationally-recognized overnight courier or by registered or certified mail,
return receipt requested and postage prepaid, addressed as follows:

	 	(a)	 	if to the Company, to:

Alon USA GP, LLC

7616 LBJ Freeway, Suite 300

Dallas, TX 75251

Telecopy number: (972) 367-3724
	 
	 	(b)	 	if to Manager, to the address of Manager set forth on the signature page hereto;

or to such other address as the party to whom notice is to be given may have furnished to the

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other in writing in accordance with the provisions of this Section 16. Any such notice or
communication shall be deemed to have been received: (i) in the case of personal delivery, on the
date of such delivery; (ii) in the case of nationally-recognized overnight courier, on the next
business day after the date sent; and (iii) if by registered or certified mail, on the third
business day following the date postmarked.

     18. Applicable Law. This Agreement shall be governed by and construed in accordance with the
laws of the State of Texas without giving effect to principles of conflicts of law.

	 	 	 	 	 	 	 	 	 

	MANAGER:	 	 	 	EMPLOYER:	 	 
	 
	 	 	 	 	 	 	 	 
	Paul Eisman	 	 	 	ALON USA GP, LLC	 	 
	 
	 	 	 	 	 	 	 	 
	/s/ Paul Eisman
 

	 	 
	 	By:

Name:
	 	/s/ Jeff D. Morris
 

Jeff Morris
	 	 
	 

	 	 	 	Title:
	 	Chief Executive Officer	 	 

8exv10w56

Exhibit 10.56

Description of Annual Bonus Plans

The Board of Directors of Alon USA Energy, Inc. (“Alon”) approved three annual bonus plans pursuant
to Alon’s Amended and Restated 2005 Incentive Compensation Plan (collectively, the “Bonus Plans”).
Annual cash bonuses under these plans are generally distributed to eligible employees in the first
or second quarter of each year based on the previous year’s performance. Each of the Bonus Plans
contains the same plan elements, which are described below. Alon’s refining and marketing employees
and Big Spring refinery employees are eligible to participate in one plan based primarily on the
performance of Alon’s Big Spring refinery. The employees of Alon’s Paramount Petroleum Corporation
subsidiary are eligible to participate in a second plan based primarily on the performance of
Alon’s California refineries. The employees at the Krotz Springs refinery are eligible to
participate in the third plan based primarily on the performance of Alon’s Krotz Springs refinery.
The bonus potential for Alon’s named executive officers is based 33.3% on the bonus plan for
employees of Alon’s Big Spring refinery, 33.3% on the bonus plan for employees of the California
refineries and 33.3% on the bonus plan for employees of the Krotz Springs refineries.

Under each bonus plan, bonus payments are based 37.5% on meeting or exceeding target reliability
measures, 37.5% on meeting or exceeding target free cash flow measures and 25% on meeting or
exceeding target safety and environmental objectives. The bonus pool available under each plan will
be calculated each year based on 20% of the aggregate direct salary expenses of the employees
eligible to participate in such plan. All of Alon’s current named executive officers are eligible
to participate in the bonus plan applicable to Alon’s refining and marketing employees. The bonus
potential for Alon’s named executive officers ranges from 65% to 100% of the respective executive
officer’s base salary, as established in each executive officer’s employment agreement.

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