Investor Presentation

May 16, 2013

- 2 - 2

Forward-Looking Statements

All statements contained in or made in connection with this presentation that are not statements of historical fact are forward-looking statements intended to be covered by the safe harbor provisions of the Securities Act of 1933 or the Securities Exchange Act of 1934. The words ―believe‖, ―intend‖, ―plan‖, ―expect‖, ―should‖, ―estimate‖, ―anticipate‖, ―potential‖, ―future‖, ―will‖ and similar terms and phrases identify forward-looking statements. Forward-looking statements reflect the current expectations of the management of Alon USA Energy, Inc. (―Alon‖) regarding future events, results or outcomes. These expectations may or may not be realized and actual results could differ materially from those projected in forward-looking statements. Alon’s businesses and operations involve numerous risks and uncertainties, many of which are beyond our control, which could result in the expectations reflected in forward-looking statements not being realized or which may otherwise affect Alon’s financial condition, results of operations and cash flows. These risks and uncertainties include, among other things, changes in price or demand for our products; changes in the availability or cost of crude oil and other feedstocks; changes in market conditions; actions by governments, competitors, suppliers and customers; operating hazards, natural disasters or other disruptions at our or third-party facilities; and the costs and effects of compliance with current and future state and federal regulations. For more information concerning factors that could cause actual results to differ from those expressed in forward-looking statements, see Alon’s Form 10-Q for the quarter ended March 31, 2013 which has been filed with the Securities and Exchange Commission and is available on the company’s web site at http://www.alonusa.com. Alon undertakes no obligation to update or publicly release the results of any revisions to any forward-looking statements that may be made to reflect events or circumstances that occur, or that we become aware of, after the date of this presentation or to reflect the occurrence of unanticipated events.

- 3 - 3

Table of Contents

I. Business Overview

II. Financial Summary

Appendix: Additional Materials

I. Business Overview

- 5 - 5

Overview of Alon Energy

Alon USA Partners,

LP

Includes the Big Spring refinery (TX) with a throughput capacity of 70,000 bpd

Includes the wholesale fuels marketing business which is integrated through the Big Spring refinery system

Markets gasoline and diesel to ~635 sites under the ALON brand, including Alon Brands stores

Krotz Springs Includes the Krotz Springs (LA) refinery with a throughput capacity of 74,000 bpd

California Includes the Paramount, Long Beach and Bakersfield refineries with a throughput capacity of 70,000 bpd

Asphalt

Owns and operates 11 asphalt terminals in the western U.S. Operations include:

— 50% ownership in Paramount Nevada Asphalt Company, and

— 50% ownership in Wright Asphalt

Second largest supplier of asphalt in California

Second largest supplier of asphalt in Texas

Retail Largest 7-Eleven licensee in the U.S. with 298 retail gasoline / convenience stores in Central and West Texas

and New Mexico (~50% fee owned)

Alon Energy conducts its operations through five business units: Big Spring Refining & Wholesale Fuels Marketing (―Alon USA

Partners, LP‖), Krotz Springs Refining (―Krotz Springs‖), California Refining (―California‖), Asphalt Marketing (―Asphalt‖), and

Retail. ALJ is the general partner and owns 81.6% of the Alon USA Partners, LP

The Company generated $524 million of Adjusted EBITDA for the LTM period ended March 31, 2013 and $157 million of

Adjusted EBITDA for 1st quarter of 20131

1 See page 27 for a reconciliation of Adjusted EBITDA to Net Income under GAAP.

- 6 - 6

Business Strategy

Refining¹

Maintain focus on safety and reliability

Run Big Spring at maximum capacity

Run Krotz Springs at maximum capacity

(using 30,000 bpd of WTI) to leverage recent

capital improvements

Improve crude flexibility in our CA refineries

via the ability to receive advantaged crude by

rail

Maintain operating expense leadership

Optimize crude slate to take advantage of regional

pricing dislocations

Optimize refined product slate to take advantage of

distillate production capacity and strong margin

environment

Maintain capital discipline and continued

investments in high return projects

Enhance branded wholesale business

Asphalt

Optimize asphalt production and 3rd party

purchases

Leverage existing distribution network

Focus in maintaining our market share in premium,

specialty asphalts products (Emulsions, Polymer

Modified Asphalts (―PMA‖) and Ground Tire Rubber

(―GTR‖) blends)

Optimize Zero-Pen shipments to the West Coast

Retail

Continue improvement of operations through

Clean TEAM efforts: remodel interior and

exterior retail sites and selectively increase

store count

Increase fuels sold under ALON brand

Increase sales of high margin food products

and inventory turns

Expand and grow the retail locations in target

markets

Optimize pricing

Operational Focus Commercial Focus

1 Refining includes Big Spring and Wholesale Marketing, Krotz Springs and the California complex.

- 7 - 7

Alon USA Strategic Advantages

Strategically Located Refineries with Advantageous Sources of Crude Supply

Significant Exposure to High Margin Distillates

Physically Integrated Retail and Wholesale Network

Diversified Operations Provide Stability

High Quality Assets with Low Operating Costs

Leading Blended and Modified Asphalt Producer

Strong Liquidity Position and Flexibility provided by Supply & Off-take Agreements at each

refinery

Experienced Management Team

- 8 - 8

California

Arizona

Texas

Oklahoma

Arkansas

Louisiana

Bakersfield

Tucson

El Paso

Nederland

Duncan

Abilene

Wichita Falls

Big Spring

Albuquerque

Bloomfield

Moriarty

Midland / Odessa

New Mexico

Nevada

Oregon

Washington

Paramount/

Long Beach

Portland

Willbridge

Richmond Beach

Elk Grove

Flagstaff

Mojave

Fernley

Tulsa

Corpus Christi

Houston

Krotz Springs

Lubbock

DFW

Third-Party Terminal

Asphalt Terminal

Refinery

Key Retail Cities

Exchange Terminal

Alon Pipelines

Third Party Pipelines

Wright JV Asphalt Terminal

Alon USA Terminal

Phoenix

Orla

South Marsh

Island Loop

Empire

Strategically Located Assets

Refinery

Capacity

(bpd)

Nelson

Complexity

Big Spring 70,000 10.8

Krotz Springs 74,000 8.3

California 70,000 TBD

- 9 - 9

Diversified Operations Provide Stability

Three separate refinery complexes provide asset and geographic diversification

Five business units (Big Spring and wholesale fuels marketing, Krotz Springs refining, California refining,

asphalt marketing and retail) provide business diversification

— Regional differences in Alon’s refining base (Louisiana, Texas and California) provide diversification

during price dislocations

— Asphalt business is typically counter-cyclical to refining environment

— Retail business provides steady and predictable cash flows

LTM March 31, 2013 Gross Margin by

Business Unit

LTM March 31, 2013 Production by

Refinery

Total Gross margin: $1,089 million Total Production: 152Mbpd

Big Spring, 59.6%

Krotz Springs, 22.1%

California, 1.3%

Asphalt, 3.7%

Retail, 13.4%

$1,089

million

Big Spring, 43.7%

Krotz Springs, 44.2%

California, 12.1%

152Mbpd

- 10 - 10

Flexible Refineries with Low Operating

Expenses

LTM March 31, 2013 Refinery Operating Expenses ($/bbl) – Mid-Continental and Gulf Coast Groups

Source: Derived from public company filings with SEC.

Note: Refinery direct expense is a per barrel measurement calculated by dividing direct operating expenses by total throughput volume.

(1) VLO Mid-Continent region includes the McKee, Ardmore, and Memphis Refineries.

(2) HFC Mid-Continent region includes the El Dorado and Tulsa Refineries.

(3) VLO Gulf Coast region includes the Corpus Christi , Port Arthur, St. Charles, Texas City, Aruba, Houston, Three Rivers and Meraux Refineries.

Mid-Continent Peer Group Gulf Coast Peer Group

$3.57 $4.41 $4.46 $4.80 $5.07 $5.34

$6.34 $6.35

$10.00

$3.57 $3.94 $4.23

VLO Mid-Continent (1)

CVICoffeyville, KS

ALJ Big Spring,TX

WNR El Paso,TX

HFC Mid-Continent (2)

DK Tyler, TX HFC Navajo,NM

CVIWynnewood,

OK

WNR FourCorners, NM

VLO GulfCoast (3)

ALJ KrotzSprings, LA

DK El Dorado,AR

- 11 - 11

Crude Differentials

Beginning in 2011, WTI related crudes have shown a substantial divergence from historical trends and

differentials for LLS and Buena Vista crudes are significantly greater than any time in past 5 years

¹ 5 Year Average of 2008 to 2012

² YTD as of Mar 2013

Louisiana Light Sweet

("LLS")

GC321

5 Year Average --$15.35

YTD 2013---$28.40

WC3111 (BV)

5 Year Average --$10.56

YTD 2013 ---$11.06

GC 211 (HSD/LLS)

5 Year Average --$8.08

YTD 2013 ---$8.20

West Texas Sour ("WTS")West Texas

Intermediate ("WTI")

Buena Vista

("BV")

5 Year Average¹ --$86.00 YTD 2013² ---$94.27

WTI - WTS 5 Year Average --$2.99

YTD 2013 ---$11.41

WTI - BV 5 Year Average --$(3.47)

YTD 2013 ---$(15.76)

LLS - WTI 5 Year Average --$7.25

YTD 2013 ---$20.22

- 12 - 12

Big Spring Refinery Overview

On November 20, 2012 Alon USA Partners, LP (―ALDW‖)

completed an initial public offering as a variable rate MLP

— Issued 11.5 million of common units raising $184 million (The public

owns an 18.4% limited partner interest in Alon Partners)

The Big Spring refinery located in Big Spring, Texas

— 70,000 bpd (~26 million bbl/year) sour crude cracking refinery

— 10.8 Nelson Complexity

Captive wholesale fuels marketing business supplies substantially

all of Alon Retail segments

Closest refinery to robust West Texas crude oil production

(Permian Basin), which provides a significant crude cost advantage

Additional benefit from running ~76% West Texas Sour (―WTS‖),

which traded at an average discount to West Texas Intermediate

(―WTI‖) of $11.41/bbl for the three months ended March 31, 2013

Product price advantage based on favorable location

— Gulf Coast refiners pay ~$2.50/bbl to ship light products to our region

Majority of the units have been rebuilt at Big Spring refinery post

February 2008 fire

— Since 2008, the Company invested ~$500 million to rebuild

equipment and make other refinery improvements

Entered into a Supply and Off-take Agreement with J. Aron in

March 2011

$7.64

20.89

23.50

28.76

$0.00

$5.00

$10.00

$15.00

$20.00

$25.00

$30.00

$35.00

2010 2011 2012 1Q 2013

$ /

bb

l

Refinery Operating Margin

80%

80% 76%76%

15%

16%21%

19%5%

4%3%

5%49,028

63,61468,946

59,476

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

80,000

2010 2011 2012 1Q 2013

bpd

WTS crude WTI crude Blendstocks

Refinery Throughput

50% 49% 50% 50%

32% 32% 32% 32%

6% 7% 6% 6%

11% 12% 11% 11%

99.1% 99.8% 99.8% 99.4%

0%

20%

40%

60%

80%

100%

2010 2011 2012 1Q 2013

Gasoline Diesel/jet Asphalt Other

Refinery Product Yield

*

* Lower throughput is due to reformer regeneration and maintenance work

- 13 - 13

Big Spring sources substantially

all of its crude oil locally from

the Permian Basin

The Permian Basin is

experiencing a drilling and

production renaissance, with

482 active drilling rigs

Lack of logistics infrastructure

limits crude oil transport to the

Gulf Coast, creating attractive

opportunities for Big Spring to

purchase at a significant

discount

¹ Baker Hughes, RigData, U.S. Energy Information Administration. Rig data as of November 2, 2012.

² Production Data obtained from RRC Production Data Query on March 27, 2013

Big Spring is in the Heart

of the Permian Basin

Permian Basin Activity Overview1

Active

Drilling Rigs

Existing pipelines

Proposed/under construction

Year Oil Produced (million bbl.)

2005 253

2006 252

2007 251

2008 260

2009 260

2010 270

2011 295

2012 312

Crude Oil Production2

- 14 - 14

Krotz Springs Refinery Overview

74,000 bpd sweet crude residual cracking refinery

8.3 Nelson Complexity

Historically processed a mix LLS and HLS type

crudes.

Access to 30,000 bpd of WTI Midland priced crude

through the AMDEL pipeline and using our existing

railcars to ship and additional 6,000 bpd of WTI

Midland priced crude oil to a railcar unloading terminal

facility at Krotz Springs

High liquid recovery of over 101%

One of the newest refineries in the U.S. (1980)¹ with

industry low operating costs

Access to domestic and foreign crude markets

through the Louisiana Offshore Oil Port (―LOOP‖)

High distillate yield capability of ~40%

Refinery Product Yield

¹ Source: US Energy Information Administration.

$2.24 $3.05

$8.30

$13.14

$0.00

$2.00

$4.00

$6.00

$8.00

$10.00

$12.00

$14.00

2010 2011 2012 1Q 2013

$ /

bb

l

Refinery Operating Margin

30% 43%

98%

99%

69% 54%2%

1%

1%

3%

39,244

59,72067,877

58,439

-5,000

15,000

35,000

55,000

75,000

2010 2011 2012 1Q 2013

bpd

WTI crude Gulf Coast sweet crude Blendstocks

Refinery Throughput

40% 42% 43% 46%

48% 46% 42% 38%

12% 13% 16% 18%

100.4% 100.6% 101.2% 102.3%

0%

20%

40%

60%

80%

100%

2010 2011 2012 1Q 2013

Gasoline Diesel/Jet Other

*

* Lower throughput is due to reformer regeneration and maintenance work

- 15 - 15

California Refineries Overview

Integrated complex consisting of the Paramount, Long Beach and Bakersfield refineries with a throughput capacity of

70,000 bpd

Operates in one of the largest distillate markets in the U.S

Since 2011 heavy West Coast crude pricing increased relative to mid-continent based crudes. This has primarily been

driven by the rapid increase in production of U.S. domestic crudes in the mid-continent region, for which logistics are not

readily available to transport to major refining regions on the U.S. Gulf Coast

The California complex used heavy crude to produce approximately 30% asphalt whose demand is at cyclical lows.

Asphalt demand is expected to rise with the passing of the new federal highway spending bill, and revival of the housing

market which is at its strongest since 2006

Operated at low throughput rates in 2010 -12 due to high crude pricing and weak asphalt demand

In the 4th quarter of 2012, ceased operations for interim period while reconfiguring crude mix from heavy to light crudes

which will allow the system to utilize its high distillate production capability (~44%) and reduce lower value heavy product

(primarily asphalt) yields

In the interim period, significantly reduced operating expenses in the California system

Submitted permit applications to allow shipment via rail of light mid-continent crudes such as Bakken, WTI to replace

heavy West Coast crudes (expect to receive permits and complete infrastructure build out during the 4th quarter of 2013)

In the longer term, the California system is expected to benefit from a significant increase in light sweet Monterey shale oil

production (the EIA estimates the Monterey shale has 20 billion barrels of recoverable resources representing 64% of the

total recoverable shale oil in the lower 48 states)

- 16 - 16

Leading Asphalt Supplier

¹ Source: Internal Alon Asphalt marketing analysis and market studies.

Operates 11 asphalt terminals in the

western U.S. Operations include:

— 50% ownership in Paramount Nevada

Asphalt Company – the largest

GTR/PMA plant in Nevada, and

— 50% ownership in Wright Asphalt

Products Company which brings

exclusive rights to Neste’s GTR

technology

Second largest supplier of asphalt in

California and Texas

Supplies advanced asphalt products such

as rubberized asphalt, PMA and GTR

— Increasingly specified by government

agencies for use in highway projects in

Texas

Strategic access to the California asphalt

market

— California and Texas are the largest

asphalt consuming states in the U.S.

— California highway budget for asphalt

is larger than in previous years

Krotz Springs

Paramount

Among U.S. Refiners:

#7 asphalt supplier in U.S.

#2 asphalt supplier West of Mississippi

#1 asphalt supplier in PADD V states

#1 Ground Tire Rubber asphalt marketer in U.S.

#1 purchaser of polymers for paving asphalt products

Houston

Tulsa

Phoenix

Flagstaff

Willbridge

(Portland)

Elk Grove

(Sacramento)

Bakersfield

Mojave

Fernley

(Reno)

Paramount /

Long Beach

Big Spring

Corpus Christi

Richmond Beach

(Seattle)

Refineries

Asphalt terminals

Wright asphalt 3rd party throughput

Legend

- 17 - 17

Summary Financial Performance

- Asphalt

2010 2011 2012 1Q 2013

WTI $/bbl. $79.41 $95.07 $94.14 94.27$

Blended Asphalt Sales (000’s tons) 780 915 842 130

Non-Blended Asphalt Sales (000’s tons) 83 181 105 22

Total Asphalt Sales (000’s tons) 863 1,096 947 152

Sales Price/ton (blended) 477$ 541$ 590$ 540$

Sales Price/ton (non blended) 326$ 327$ 372$ 392$

Asphalt Margin/ton 51$ 27$ 43$ 62$

Polymer Modified Asphlat (000’s tons) 56 33 80 4

Ground Tire Rubber Asphalt (000’s tons) 31 87 118 8

Emulsions (000’s tons) 86 67 51 4

Total Speciality Asphalt (000’s tons) 173 187 249 16

Speciality Asphalt % of total sales volumes 25% 17% 26% 11%

Speciality Asphalt Sales price $/ton 569$ 569$ 611$ 483$

Speciality Asphalt Realizations % of WTI 128% 107% 116% 92%

Paving Grade Asphalt Realizations % of WTI 99% 93% 101% 95%

- 18 - 18

Alon Energy’s retail business unit is the

largest 7-Eleven licensee in the U.S. with 298

stores (~50% fee owned) in Central and West

Texas and New Mexico

The retail business unit has nearly doubled its

store count since 2006

Recently completed re-branding effort from

FINA branded gasoline stations to ALON

brand

Retail Asset Overview

Location Total

Big Spring, Texas 8

Wichita Falls, Texas 11

Waco, Texas 11

Midland, Texas 17

Lubbock, Texas 21

Albuquerque, New Mexico 23

Odessa, Texas 35

Abilene, Texas 41

El Paso, Texas 83

Other locations in Central and West Texas 48

Total Stores 298

Physically Integrated Retail Network

- 19 - 19

Attractive Retail Store Economics

Merchandise Sales Retail Fuel Sold

142.2

156.7

170.8 173.9

0

20

40

60

80

100

120

140

160

180

200

$0.00

$0.05

$0.10

$0.15

$0.20

$0.25

2010 2011 2012 LTM 1Q 2013

Gallons Sold (in millions) Fuel Margin ($ per gallon)

281.7

298.2

315.1 314.9

25.0%

26.0%

27.0%

28.0%

29.0%

30.0%

31.0%

32.0%

33.0%

34.0%

$260

$270

$280

$290

$300

$310

$320

2010 2011 2012 LTM 1Q 2013

Merch Sales (in $ millions) Merch Gross Profit % of Revenue

- 20 - 20

Initial Public Offering

- Alon USA Partners, LP (NYSE: ALDW)

Completed initial public offering of Big Spring and Wholesale Marketing via a Master Limited

Partnership structure under the ticker ―ALDW‖ on the NYSE on November 20, 2012 - Initial issue of 18.4% of common units to public at offer price of $16.0/unit raising $184 million of gross

proceeds

- Market value of equity at IPO - $1.0 billion

- Net debt at IPO: $305 million

- Enterprise value at IPO: $1.3 billion

$5

$10

$15

$20

$25

$30

$35

Jan-12 Feb-12 Mar-12 Apr-12 May-12 Jun-12 Jul-12 Aug-12 Sep-12 Oct-12 Nov-12 Dec-12 Jan-13 Feb-13 Mar-13 Apr-13 May-13

ALJ & ALDW Stock Price (as of May 7, 2013)

ALJ Closing Price ALDW Closing Price

- 21 - 21

Debt Reduction

In the 4th quarter of 2012 we

reduced net debt by $282 million

of which: – $171 million from the proceeds of

IPO of ALDW, and

– Additional reduction in debt with

cash flows from operations

In the 1st quarter of 2013 we

further reduced by net debt by

$137 million

Total net debt reduction over 12

months period ending March 31,

2013 was $530 million

0

200

400

600

800

1,000

1Q-12 2Q-12 3Q-12 4Q-12 1Q-13

$ m

illio

ns

Net Debt

(in $ millions) 1Q-12 2Q-12 3Q-12 4Q-12 1Q-13

Total Debt 914 874 799 587 586

Net Debt 864 817 753 471 334

II. Financial Summary

- 23 - 23

Summary Financial Performance

- Refining

*Note: In Q3 2011 the WC 3-2-1 (Buena Vista) benchmark was changed to WC 3-1-1-1 (Buena Vista)

2010 2011 2012 1Q 2013

Pricing Statistics:

GC 3-2-1 $8.22 $23.37 $27.43 $ 28.40

GC 2-1-1 (HSD/LLS) $5.26 $7.00 $11.29 $ 8.20

WC 3-1-1-1 (Buena Vista)* $8.34 $9.20 $13.08 $ 11.06

Operating Statistics:

Big Spring Refinery:

Throughput (bpd) 49,028 63,614 68,946 59,476

Operating margin/bbl. $7.64 $20.89 $23.50 $ 28.76

Operating expense/bbl. $5.05 $4.23 $4.00 $ 5.68

California Refinery:

Throughput (bpd) 17,596 22,815 17,877 N/A

Operating margin/bbl. $1.08 ($1.31) $2.36 N/A

Operating expense/bbl. $7.73 $7.32 $12.59 N/A

Krotz Springs Refinery:

Throughput (bpd) 39,244 59,720 67,877 58,439

Operating margin/bbl. $2.24 $3.05 $8.30 $13.14

Operating expense/bbl. $4.36 $3.67 $3.85 $4.42

- 24 - 24

Historical Crack Spreads

$7.64

$20.89

$23.50

$28.76

$2.24 $3.05

$8.30

$13.14

$1.08

($1.31)

$2.36

$8.22

$23.37

$27.43 $28.40

$5.26 $7.00

$11.29

$8.20

$8.34

$9.20

$13.08

$11.06

($5.00)

$0.00

$5.00

$10.00

$15.00

$20.00

$25.00

$30.00

$35.00

2010 2011 2012 1Q 2013

($ /

bb

l.)

Big Spring Operating Margin Krotz Springs Operating Margin California Operating Margin

Historical Gulf Coast 321 Crack Spread Historical Gulf Coast 211 Crack Spread (LLS) Historical West Coast 3111 Crack Spread (BV)

- 25 - 25

Historical Capex

Capital and Turnaround Expenditures by Type ($millions)

Capital and Turnaround Expenditures by Asset ($millions)

$25 $23 $32

$7

$10 $21 $18

$4

$16

$56 $30

$1

$5

$17

$14

$1

$2

$3

$9

$2

$2

$2

$2

$60

$122 $105

$14

$0

$20

$40

$60

$80

$100

$120

$140

2010 2011 2012 1Q 2013

Big Spring Krotz Springs California Retail Asphalt Other

$13 $10 $11 $5

$26 $31

$53

$6

$21

$82

$15

$2

$60

$122

$105

$14

$0

$20

$40

$60

$80

$100

$120

$140

2010 2011 2012 1Q 2013

Chemcat & Turnaround Regulatory & Sustaining Growth

Appendix

- 27 - 27

Adjusted EBITDA Reconciliation

Note: Adjusted EBITDA per press release

(in $ 000's) 2010 2011 2012 1Q 2013

Net Income (122,932) 42,507 79,134 54,184

Non-controlling interest in income (loss) of subsidiaries (9,641) 1,241 11,463 19,467

Income tax expense (benefit) (90,512) 18,918 49,884 30,590

Interest expense 94,939 88,310 129,572 21,292

Depreciation and Amortization 102,096 113,730 121,929 31,163

Gain on bargain purchase (17,480) - - -

(Gain) loss on disposition of assets (945) (729) 2,309 (18)

Unrealized (gains) losses on commodity swaps - (31,936) 31,936 -

(Gain) loss on heating oil call option crack spread contracts - 36,280 7,297 -

Adjusted EBITDA (44,475) 268,321 433,524 156,678