Alon USA Partners, LP

Table of Contents Index to Financial Statements Filed pursuant to Rule 424(b)(4) SEC File No. 333-183671 10,000,000 Common Units Representing Limited Partner Interests Alon USA Partners, LP This is the initial public offering of our common units representing limited partner interests. We are offering 10,000,000 common units in this offering. Prior to this offering, there has been no public market for our common units. Our common units have been approved for listing on the New York Stock Exchange under the symbol “ALDW.” Investing in our common units involves risks. See “Risk Factors” beginning on page 18. These risks include the following: • We may not have sufficient available cash to pay any quarterly distribution on our common units. • The price volatility of crude oil, other feedstocks, refined products and fuel and utility services may have a material adverse effect on our earnings, profitability and cash flows, and our ability to make distributions to unitholders. • Changes in the WTI—Brent or Cushing WTI—Midland WTS differentials or the easing of logistical and infrastructure constraints at Cushing, Oklahoma could adversely affect the crude oil cost advantage that has been in our favor, which could negatively affect our profitability. • The amount of our quarterly cash distributions, if any, will vary significantly both quarterly and annually and will be directly dependent on the performance of our business. Unlike most publicly traded partnerships, we will not have a minimum quarterly distribution or employ structures intended to consistently maintain or increase distributions over time. • Our unitholders have limited voting rights and are not entitled to elect our general partner or our general partner’s directors. • You will incur immediate and substantial dilution in net tangible book value per common unit. • Our tax treatment depends on our status as a partnership for U.S. federal income tax purposes, as well as our not being subject to a material amount of entity-level taxation by individual states. If the IRS were to treat us as a corporation for federal income tax purposes or we were to become subject to material additional amounts of entity-level taxation for state tax purposes, then our cash available for distribution to you could be substantially reduced. • You will be required to pay taxes on your share of our income even if you do not receive any cash distributions from us. Neither the Securities and Exchange Commission nor any other regulatory body has approved or disapproved of these securities or passed upon the accuracy or adequacy of this prospectus. Any representation to the contrary is a criminal offense. Per Common Unit Total Initial public offering price $ 16.00 $160,000,000 Underwriting discount $ 1.12 $ 11,200,000 Proceeds, before expenses, to Alon USA Partners, LP $ 14.88 $148,800,000 To the extent that the underwriters sell more than 10,000,000 common units, the underwriters have the option to purchase up to an additional 1,500,000 common units at the initial public offering price less the underwriting discount. The underwriters expect to deliver the common units against payment in New York, New York on or about November 26, 2012. Goldman, Sachs & Co. Credit Suisse Citigroup Jefferies Macquarie Capital Tudor, Pickering, Holt & Co. Prospectus dated November 19, 2012. Table of Contents Index to Financial Statements Table of Contents Index to Financial Statements TABLE OF CONTENTS PROSPECTUS SUMMARY 1 Alon USA Partners, LP 1 Competitive Strengths 3 Business Strategy 4 Refining Industry Overview 5 Risk Factors 6 Our Relationship with Alon Energy 6 Our Management 6 Conflicts of Interest and Fiduciary Duties 7 About Us 7 The IPO Transactions 7 Organizational Structure 9 The Offering 10 Summary Historical Combined and Pro Forma Combined Financial and Operating Data 14 Non-GAAP Financial Measure 17 RISK FACTORS 18 Risks Inherent in Our Business 18 Risks Inherent in an Investment in Us 33 Tax Risks 41 CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS 45 USE OF PROCEEDS 46 CAPITALIZATION 47 DILUTION 48 CASH DISTRIBUTION POLICY AND RESTRICTIONS ON DISTRIBUTIONS 50 General 50 Unaudited Pro Forma Available Cash 52 Estimated Cash Available for Distribution for the Twelve Months Ending September 30, 2013 54 Forecast Assumptions and Considerations 58 HOW WE MAKE CASH DISTRIBUTIONS 64 Distributions of Available Cash 64 SELECTED HISTORICAL COMBINED AND PRO FORMA COMBINED FINANCIAL DATA 65 MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS 67 Overview 67 Outlook 68 Factors Affecting Comparability of Our Historical Results 68 Factors Affecting Our Results of Operations 70 Results of Operations 71 Nine Months Ended September 30, 2012 Compared to Nine Months Ended September 30, 2011 73 Year Ended December 31, 2011 Compared to Year Ended December 31, 2010 74 Year Ended December 31, 2010 Compared to Year Ended December 31, 2009 75 Liquidity and Capital Resources 76 Cash Flows 77 Amended and Restated Revolving Credit Facility 78 Intercompany Debt 79 New Term Loan Facility 79 Capital Spending 80 Contractual Obligations 80 Off-Balance Sheet Arrangements 80 i Table of Contents Index to Financial Statements Critical Accounting Policies 81 Quantitative and Qualitative Disclosures About Market Risk 82 BUSINESS 84 Our Company 84 Competitive Strengths 85 Business Strategy 87 Refining Industry Overview 88 Our Refinery 90 Competition 96 Trade Names, Service Marks and Trademarks 97 Governmental Regulation and Legislation 97 Seasonality 100 Employees 100 Properties and Insurance 100 Legal Proceedings 100 MANAGEMENT 101 Management of Alon USA Partners, LP 101 Executive Officers and Directors 102 EXECUTIVE COMPENSATION 107 Executive Compensation 107 Director Compensation 111 SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT 112 CERTAIN RELATIONSHIPS AND RELATED PARTY TRANSACTIONS 113 Distributions and Payments to Alon Energy and its Affiliates 113 Agreements with Alon Energy 114 Other Transactions with Related Parties 116 CONFLICTS OF INTEREST AND FIDUCIARY DUTIES 117 Conflicts of Interest 117 Fiduciary Duties of Our General Partner 122 Related Party Transactions 124 DESCRIPTION OF THE COMMON UNITS 125 Our Common Units 125 Transfer Agent and Registrar 125 Transfer of Common Units 125 Listing 126 THE PARTNERSHIP AGREEMENT 127 Organization and Duration 127 Purpose 127 Capital Contributions 127 Adjustments to Capital Accounts Upon Issuance of Additional Common Units 127 Voting Rights 128 Applicable Law; Forum, Venue and Jurisdiction 129 Limited Liability 129 Issuance of Additional Partnership Interests 130 Amendment of Our Partnership Agreement 131 Merger, Consolidation, Conversion, Sale or Other Disposition of Assets 133 Termination and Dissolution 134 Liquidation and Distribution of Proceeds 134 Withdrawal or Removal of Our General Partner 134 Transfer of General Partner Interest 135 Transfer of Ownership Interests in Our General Partner 136 Change of Management Provisions 136 ii Table of Contents Index to Financial Statements Call Right 136 Non-Citizen Assignees; Redemption 137 Non-Taxpaying Assignees; Redemption 137 Meetings; Voting 137 Status as Limited Partner or Assignee 138 Indemnification 138 Reimbursement of Expenses 138 Books and Reports 139 Right to Inspect Our Books and Records 139 Registration Rights 140 UNITS ELIGIBLE FOR FUTURE SALE 141 MATERIAL U.S. FEDERAL INCOME TAX CONSEQUENCES 143 Taxation of the Partnership 143 Tax Consequences of Unit Ownership 145 Tax Treatment of Operations 149 Disposition of Units 150 Uniformity of Units 152 Tax-Exempt Organizations and Other Investors 153 Administrative Matters 153 State, Local and Other Tax Considerations 155 INVESTMENT IN ALON USA PARTNERS, LP BY EMPLOYEE BENEFIT PLANS 156 UNDERWRITING 157 VALIDITY OF OUR COMMON UNITS 162 EXPERTS 162 WHERE YOU CAN FIND MORE INFORMATION 162 ALON USA PARTNERS, LP INDEX TO COMBINED FINANCIAL STATEMENTS F-1 APPENDIX A—AMENDED AND RESTATED AGREEMENT OF LIMITED PARTNERSHIP OF ALON USA PARTNERS, LP A-1 APPENDIX B—GLOSSARY OF INDUSTRY TERMS USED IN THIS PROSPECTUS B-1 You should rely only on the information contained in this prospectus, any free writing prospectus prepared by or on behalf of us or any other information to which we have referred you in connection with this offering. We have not, and the underwriters have not, authorized any other person to provide you with information different from that contained in this prospectus. Neither the delivery of this prospectus nor sale of our common units means that information contained in this prospectus is correct after the date of this prospectus. This prospectus is not an offer to sell or solicitation of an offer to buy our common units in any circumstances under which the offer or solicitation is unlawful. Through and including December 14, 2012 (the 25th day after the date of this prospectus), all dealers effecting transactions in these securities, whether or not participating in this offering, may be required to deliver a prospectus. This is in addition to a dealer’s obligation to deliver a prospectus when acting as an underwriter and with respect to an unsold allotment or subscription. We have not authorized anyone to provide any information or to make any representations other than those contained in this prospectus or in any free writing prospectuses we have prepared. We take no responsibility for, and can provide no assurance as to the reliability of, any other information that others may give you. This prospectus is an offer to sell

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