Investor UpdateMay 2020

2

Regarding Forward-Looking Statements

Statements contained in this press release that are not historical facts are forward-looking statements. Forward-looking statements relate to current expectations regarding our future financial condition, performance and results of operations, planned capital expenditures, long-term objectives of management, supply and demand, pricing trends and market forces, and integration plans and expected benefits of transactions and are often identified by the use of words and phrases such as "anticipate," "believe," "continue," "could," "estimate," "expect," "intend," "may," "plan," "predict," "project," "should," "will," "would," "is likely to," "is expected to" or "will continue," or the negative of these terms or other comparable terminology. All forward-looking statements are subject to risks and uncertainties that could cause actual results to differ from those projected. Other factors that may cause actual results to differ from the forward-looking statements contained in this release and that may affect the company's prospects in general include, but are not limited to, (a) general economic and business conditions and the competitive conditions in the baked foods industry, including promotional and price competition, (b) changes in consumer demand for our products, including changes in consumer behavior, trends and preferences, including health and whole grain trends, and the movement toward more inexpensive store-branded products, (c) the success of productivity improvements and new product introductions, (d) a significant reduction in business with any of our major customers including a reduction from adverse developments in any of our customer's business, (e) fluctuations in commodity pricing, (f) energy and raw material costs and availability and hedging and counterparty risk, (g) our ability to fully integrate recent acquisitions into our business, (h) our ability to achieve cash flow from capital expenditures and acquisitions and the availability of new acquisitions that build shareholder value, (i) our ability to successfully implement our business strategies, including those strategies the company has initiated under Project Centennial, which may involve, among other things, the integration of recent acquisitions or the acquisition or disposition of assets at presently targeted values, the deployment of new systems and technology and an enhanced organizational structure, (j) consolidation within the baking industry and related industries, (k) disruptions in our direct-store delivery system, including litigation or an adverse ruling from a court or regulatory or government body that could affect the independent contractor classification of our independent distributors, (l) increasing legal complexity and legal proceedings that we are or may become subject to, (m) product recalls or safety concerns related to our products, and (n) the failure of our information technology systems to perform adequately, including any interruptions, intrusions or security breaches of such systems. The foregoing list of important factors does not include all such factors, nor necessarily present them in order of importance. In addition, you should consult other public disclosures made by the company, including the risk factors included in our most recently filed Annual Report on Form 10-K and Quarterly Reports on Form 10-Q filed with the Securities and Exchange Commission ("SEC") and disclosures made in other filings with the SEC and company press releases, for other factors that may cause actual results to differ materially from those projected by the company. We caution you not to place undue reliance on forward-looking statements, as they speak only as of the date made and are inherently uncertain. The company undertakes no obligation to publicly revise or update such statements, except as required by law.

Flowers Investment Highlights

3

Priorities to Drive Margins

Leading Brands in a Large and Stable

Market

Focus on Shareholder

Returns

Executing on strategies designed to manage costs, leverage data-driven insights, and reposition our company for success

Operate the #1 organic bread, loaf bread, and gluten-free bread brands in the U.S. in Dave’s Killer Bread, Nature’s Own, and Canyon Bakehouse.

Dividend paid in 71 consecutive quarters and a management team that is aligned with shareholder interests

Growth in Underdeveloped

Markets

Strategy developed to capitalize on underdeveloped regions and build share in $32-billion fresh bakery market

BusinessOverview

Business Overview

Value Creation Strategy

Financial Review & Outlook

#1 loaf bread brand

#1 organic bread brand

#1 and FASTEST GROWING gluten-free bread brand in U.S.

98% consumer awareness

Iconic snack cakes since 1914

5

Leading Fresh Bakery Brands Drive Our Business

Non-retail & other24%

Branded Breads50%

Branded Snack Cakes10%

Branded retail60%

SALES OVERVIEW BRAND PORTFOLIO HIGHLIGHTS

Source: Internal Sales Data Warehouse 52 Weeks Ended 12/28/2019

Store branded

retail16%

FY19 Sales

$4.1B

6

Fresh Bakery Market Overview

$23.7 $23.9 $24.0 $24.3 $24.7

$-

$5.0

$10.0

$15.0

$20.0

$25.0

$30.0

2015 2016 2017 2018 2019

$ in Billions

Large and stable market

$32.4B FRESH BAKERY MARKETRETAIL & FOODSERVICE US FRESH BAKERY - RETAIL OUTLETS

$7.7BFoodservice1

1. Data for Retail Outlets sourced from IRI. FY 2019.2. Data for Foodservice sourced from Techonomic 2019.

$24.7BRetail Breads,

Snack Cakes, Tortillas2

7

Improving Competitive Position

18.2% Flowers

29.8% BBU/

Sara Lee

6.0% Pepperidge

Farm

25.6% Independent

bakers

20.4% Store brands

0.6 0.5

0.4

0.8 0.9 0.9

0.8

0.3

1.3

18Q1 18Q2 18Q3 18Q4 19Q1 19Q2 19Q3 19Q4 20Q1

IRI Flowers custom data base Total US MultiOutlet – 20Q1

#2 Baker and Growing Share

FRESH PACKAGED BREADS SHARE FLOWERS MARKET SHARE CHANGE

$232.1 $257.3 $267.3

$294.1 $320.3

FY15 FY16 FY17 FY18 FY19

8

Smart, Disciplined M&A Driving Share Gains

Organic Segment Source: Flowers Custom Database – IRi Total US Multi Outlet + C StoreGluten-free Segment Source: IRI Custom Scan Data Total US Multi Outlet + C Store combined with SPINS Total US Natural & Specialty Gourmet Channel

Capturing growth by anticipating shifting consumer preferences

TOTAL ORGANIC FRESH PACKAGED BREADS

TOTAL GLUTEN-FREE FRESH PACKAGED BREADS

$284.8

$366.7

$499.3

$614.7

$696.3

FY15 FY16 FY17 FY18 FY19

FLO Share 64.7% FLO

Share 25.3%

$ in Millions

Underdeveloped Markets Provide Upside

9 IRI Flowers custom data base Total US Multi Outlet + Convenience – 19Q4

15.2

35.2

25.8

23.7

5.3

27.543.1

24.2

25.7

25.9

28.1

20.3

8.5

32.7

37.4

21.4

FRESH PACKAGED BREADS CATEGORY DOLLAR SHARE IN THE US

■ Flowers■ Bimbo USA

■ Store Brands■ Independents

Substantial room to grow share

CALIFORNIA & WEST

MID SOUTH, SOUTH CENTRAL, & SOUTHEAST

NORTHEASTGREAT LAKES & PLAINS

Market Share Opportunities Beyond Loaf Breads

$4.0

$2.0 $2.0

$3.4

$1.6

$0.4 $0.3 $0.2$0.0

$0.5

$1.0

$1.5

$2.0

$2.5

$3.0

$3.5

$4.0

$4.5

Traditional Loaf Specialty/Premium Loaf Sandwich Bun/Roll Breakfast/Dinner/Other

Billi

ons

Total Branded FLO

Brand extensions and M&A in adjacent segments #1 in

Traditional Loaf

10 IRI Flowers custom data base FY19

DKB extension driving share gains in breakfast segment

11

Well Positioned as E-Commerce Accelerates

$240.5 $266.0

$395.6

$595.7

$-

$100.0

$200.0

$300.0

$400.0

$500.0

$600.0

$700.0

FY16 FY17 FY18 FY19

Fresh Bakery E-Commerce Channel Facts:

• $595.7M channel, +51% YOY growth1

• E-commerce is ~4% of total fresh bread & rolls category2

• Flowers’ leading brands provide a competitive advantage in the E-commerce channel

FRESH BREAD & ROLLS E-COMMERCE CHANNEL

1. IRI Syndicated E Market Highlights, FY192. IRI Syndicated E Market Highlights, FLO dollar share for FY19

$ in Millions

Broad Scale is a Platform for Profitable Growth

46Operating bakeries

of the U.S. population

Warehouse distribution NATIONWIDE

Channels servedGrocery / MassNatural & OrganicClub & Dollar, C-storeE-commerceFoodservice & Vending

9,700 employees

5,590IDP* territories

85%

Direct-store-distribution access to

12Information as of year-end fiscal 2019* “IDP” – Independent Distributor Partners

Value CreationStrategy

Business Overview

Value Creation Strategy

Financial Review & Outlook

PRIORITIZE MARGINS• Reduce organizational and

indirect costs

• Strategic pricing

• Optimize portfolio and network

DEVELOP TEAM• Restructure around

priorities, drive execution

• Add critical capabilities to build brands, manage costs, and deliver insights

SMART M&A• Proactive M&A in product and

geographic adjacencies in the baked foods category

• Pivot portfolio to growing bakery segments

Project Centennial Defined Our Strategic Priorities

14

FOCUS ON BRANDS• Prioritize national brands

• Invest in brand growth and innovation

• Streamline product assortment

We're Delivering on the Playbook

15

HIGHLIGHTS2017 2018 2019

TEAM Designed new organization and hired CMO

Stood up business units and created PG&S*,

FP&A* teams

Updated incentive comp framework

BRANDS Launched DKB breakfast line

Launched Nature’s Own Perfectly Crafted line

New ads for Nature’s Own, Wonder

MARGINS~$32M gross savings primarily from lower

indirect spend

~$48M gross savings primarily from headcount

reductionStrategic pricing

M&A Created S&V* team Acquired Canyon Bakehouse Hired VP Corp Dev

* PG&S: Purchased Goods & Services, FP&A: Financial Planning & Analysis, S&V: Strategy & Ventures

New Org Structure Enables Execution on Strategic Priorities

16

Aligned with Strategy

National

Clarified Portfolio Roles

Centralized

Metrics that Matter

Predictive Analytics

Regional

LEGACY ORGANIZATION NEW WAYS OF WORKING

Locally Managed

Duplicated

Overlapping

Inconsistent

Historical Reporting

Perspective

Brand Strategies

Cost Management

Responsibilities

KPIs

Insights

Providing a foundation for the company we want to become

Innovation and Marketing Investments in Key Brands

17

Wonder Honey Buns drive in-store

displays

New media campaigns for Nature’s Own and Wonder

Power of strategic partnerships: USO/Wonder/Tastykake

Nature’s Own Perfectly Crafted driving brand share growth

Tastykake Scoop Shop innovation driving

brand growth

Dave’s Killer Bread national launch of

organic English Muffins

Canyon Bakehouse #lovebreadagain campaign encourages fans to look for

new Stay Fresh items

Prioritizing Margin with Portfolio, Network Review

18

Drive profitability with…

Orient the Portfolio to … Optimize Network for …

• High-potential brands

• Disruptive innovation

• Value-over-volume

• Strategic customers

• Underdeveloped segments

• Today’s customer trends

• National scale

• Omni-channel

• Reduced complexity

• Workforce productivity

Higher brand value

Improved marketing ROI

Profitable volume growth

Capacity utilization

Distribution efficiencies

More scalable cost structure

19

Pursue Smart M&A in Adjacencies

Disciplined approach to M&A to expand position and diversify in high-growth bakery categories GROW IN-STORE

BAKERY/DELI• Grow specialty brands

on the store perimeter

• Focus on platform assets that bring new capabilities

BUILD ON LEADING FOODSERVICE POSITION• Expanding share of growing

specialty products

• Leverage scale to be a strategic partner with foodservice customers

GROW BAKED SNACKS• Evolve cake strategy

to leverage dual-brand capabilities

• Further diversify into snacking

Financial Review & Outlook

Business Overview

Value Creation Strategy

Financial Review & Outlook

Q1 2020 Financial Review

21(1) Earnings before interest, taxes, depreciation & amortization, adjusted for matters affecting

comparability. See non-GAAP reconciliations at the end of this presentation. (2) Adjusted for matters affecting comparability. See non-GAAP

reconciliations at the end of this presentation.

NET SALES $1,349.4B +6.8% v PY• Price/Mix +6.2%; Volume +0.6%

• The COVID-19 pandemic drove growth in branded retail offset by declines in non-retail

CASH FLOWS• Cash from Ops = $106.2 million

• Capex = $21.7 million

• Dividends = $40.3 million

• $203.8M increase in net borrowings driven by $200M related to COVID-19

NET INCOME $(5.8)M v $65.9M PYADJ. EBITDA1 $163.3M +19.0% v PY

• Adj. EBITDA was 12.1% of sales, up 120 bps

• Adj. EBITDA increased primarily due to favorable price/mix, lower ingredient and packaging costs, and lower stales, offset partially by higher distributor distribution fees and workforce-related costs

GAAP DILUTED EPS $(0.03) -$0.34 v PYADJ. DILUTED EPS2 $0.41 +$0.09 v PY

• GAAP EPS decreased primarily due to a $0.41 non-cash charge related to pension plan termination

• Adj. EPS increased primarily due to higher sales and improved price/mix related to COVID-19

22

Three Areas of Focus to Improve Profitability

1. Optimizing the portfolio and streamlining the supply chain

• Completed review of supply chain, which included development of more holistic customer and product profitability tool

• Moving forward with actionable insights and formulating specific plans

2. Reinvigorating and investing in the cake business

• Developed improvement plan, including new investments, for Navy Yard bakery

• Focusing on strategic volume growth to drive cost absorption, reducing complexity through SKU rationalize, identifying additional distribution opportunities, innovating

3. Stabilizing and growing the foodservice business

• Using product profitability tool to make more informed decisions around pricing and which product lines to grow

• Focusing on winning new business and increasing customer engagement to drive growth going forward

FY 2020 Guidance (Provided May 13, 2020)

231. Week 53 expected to contribute 1.5% of overall sales growth.2. Adjusted for matters affecting comparability. See non-GAAP reconciliations at the end of this presentation.

Fiscal 2020 Considerations:

• Category volume elasticities

• Commodity market volatility may affect promotional environment

• Labor markets remain tight with higher wages

• Higher bakery workforce turnover is driving reduced manufacturing efficiencies

• Freight costs remain elevated

REVENUE CHG(1) ADJ EPS(2)

OTHER

+2.0% to +4.0% $1.00 to $1.08

Depreciation & amortization —$140 to $145 million

Other pension expense —Approx. $2 million

Net interest expense —$8 to $10 million

Effective tax rate —Approx. 24.0%

Diluted shares outstanding —Approx. 212.5 million

Capital expenditures —$95 to $105 million

Project Centennial Roadmap

FY 2017 – 2018 FY 2019 & Beyond

Focus• Generate savings• Design future organization

• Invest in growth• Leverage capabilities

Targets• Sales growth: flat to +2%

• EBITDA margins: ~12% to 13%

• Sales growth: 3% to 4%

• EBITDA margins: ~13% to 14%

ProgressUpdate/Commentary

Gross savings of $80M

New org structure in place

Sales growth on-target

× Margins impacted byinflationary headwinds

• Sales growth from DKB, Canyon, strategic pricing

• Margin targets pressured by product mix, soft volumes, inflation, competitive environment

• Margin target timeline extended beyond 2021, enabled by multi-year portfolio and network optimization initiatives

24

Financial Progress Impacted by Inflationary Pressures

25

Taking action to:

• Rationalize pricing

• Reduce stales & scrap

• Improve efficiencies

• Build a career-focused team

• Prioritize value over volume

• Address network complexity

% CHANGE: FY16 THROUGH FY19

5.0%6.3%

10.3%

12.8%

3.3%

-5.5%

-7.0%

-5.0%

-3.0%

-1.0%

1.0%

3.0%

5.0%

7.0%

9.0%

11.0%

13.0%

Sales Ingredients &Packaging

ProductionLabor

Shipping &Transportation

Indirect &Other

Adj EBITDA*

Delivered topline target

Leveraged indirect costs

* Earnings before interest, taxes, depreciation & amortization, adjusted for matters affecting comparability. See non-GAAP reconciliations at the end of this presentation.

26

Track Record of Growing Free Cash Flow & Dividends

* Operating Cash flow minus Capital Expenditures. See non-GAAP reconciliations at the end of this presentation.Note: FY03, FY08, FY14 were 53 weeks.

$-

$50

$100

$150

$200

$250

$300

FY03 FY04 FY05 FY06 FY07 FY08 FY09 FY10 FY11 FY12 FY13 FY14 FY15 FY16 FY17 FY18 FY19

Free Cash Flow* Dividends Paid

Strong free cash flow growth supports investments in the business, M&A strategy and capital returns

$ in Millions

FREE CASH FLOWS AND DIVIDEND GROWTH

Top Line Drivers

• Market share gains

• Strategic acquisitions

Cash Flow Drivers

• Growing sales

• Focus on cash margins

• Predictable capex

Balanced Capital Allocation

27 *53-week year

Capital Allocation Principles:

• Capex to support core business growth

• Maintain investment grade credit rating

• Support strong dividend

• Smart, disciplined acquisitions

• Opportunistic share repurchases

$102 $120 $131 $141 $150 $160

$39 $7 $126 $3 $2 $7

$395

$200

14FY* 15FY 16FY 17FY 18FY 19FY

Dividends Share Repurchases Cash for Acquisitions

$ in Millions

CAPITAL ALLOCATION

28

Investment-Grade Credit Rating Commitment

MAINTAINING FLEXIBILITY TO CAPITALIZE ON VALUE-CREATING OPPORTUNITIES

$984 $928

$805

$980 $867

15FY 16FY 17FY 18FY 19FY

Total Debt (ex-lease liabilities)

Track-record of debt reduction following acquisitions

Aggregate Maturities at 19FY (Maturities)*

At 19FY, leverage ratio of 2.0X, $613M available liquidity on undrawn borrowing arrangements

*Maturities exclude unamortized debt discount and issuance costs

$4 $26

$442

$- $-

$400

20FY 21FY 22FY 23FY 24FY 25FY+

(Amounts in millions)

29

Our VisionAs America’s premier baker, we craft foods that make people smile. We are driven by a passion to boldly grow our business through inspiring leadership, teamwork, and creativity.

2019

1919

1968

1968 to 2018

One family-owned bakery in Thomasville, GA

More than 100 acquisitions

Listed publicly as FLO

30

Regarding Non-GAAP Financial Measures

The company prepares its consolidated financial statements in accordance with U.S. generally accepted accounting principles (GAAP). However, from time to time, the company may present in its public statements, press releases and SEC filings, non-GAAP financial measures, such as EBITDA, adjusted EBITDA, EBITDA margin, adjusted EBITDA margin, adjusted net income, adjusted operating income, adjusted EPS, adjusted income tax expense, adjusted selling, distribution and administrative expenses (SD&A), gross margin excluding depreciation and amortization and the ratio of net debt to adjusted EBITDA. The reconciliations attached provide reconciliations of the non-GAAP measures used in this presentation or release to the most comparable GAAP financial measure. The company's definitions of these non-GAAP measures may differ from similarly titled measures used by others. These non-GAAP measures should be considered supplemental to, and not a substitute for, financial information prepared in accordance with GAAP. The company defines EBITDA as earnings before interest, taxes, depreciation and amortization. The company believes that EBITDA is a useful tool for managing the operations of its business and is an indicator of the company's ability to incur and service indebtedness and generate free cash flow. EBITDA is used as the primary performance measure in the company's 2014 Omnibus Equity and Incentive Compensation Plan. Furthermore, pursuant to the terms of our credit facility, EBITDA is used to determine the company's compliance with certain financial covenants. The company also believes that EBITDA measures are commonly reported and widely used by investors and other interested parties as measures of a company's operating performance and debt servicing ability because EBITDA measures assist in comparing performance on a consistent basis without regard to depreciation or amortization, which can vary significantly. EBITDA is also a widely-accepted financial indicator of a company's ability to incur and service indebtedness. EBITDA should not be considered an alternative to (a) income from operations or net income (loss) as a measure of operating performance; (b) cash flows provided by operating, investing and financing activities (as determined in accordance with GAAP) as a measure of the company's ability to meet its cash needs; or (c) any other indicator of performance or liquidity that has been determined in accordance with GAAP. The company defines adjusted EBITDA, EBITDA margin, adjusted EBITDA margin, adjusted net income, adjusted operating income, adjusted EPS, adjusted income tax expense, adjusted SD&A expenses, respectively, to further exclude, as applicable, the impact of pension plan settlements and other costs, loss or recovery on inferior ingredients, restructuring and related impairment charges, Project Centennial consulting costs, asset impairment charges, lease terminations and legal settlements, costs related to executive retirement, acquisition-related costs, and multi-employer pension plan withdrawal costs. Adjusted net income and adjusted income tax expense also excludes the impact of tax reform. The company believes that these measures, when considered together with its GAAP financial results, provides management and investors with a more complete understanding of its business operating results, including underlying trends, by excluding the effects of certain charges. The ratio of debt to EBITDA is used as a measure of financial leverage employed by the company. Gross margin excluding depreciation and amortization is used as a performance measure to provide additional transparent information regarding our results of operations on a consolidated and segment basis. Changes in depreciation and amortization are separately discussed and include depreciation and amortization for materials, supplies, labor and other production costs and operating activities. Presentation of gross margin includes depreciation and amortization in the materials, supplies, labor and other production costs in accordance with GAAP. Our method of presenting gross margin excludes the depreciation and amortization components, as discussed above. The reconciliations attached provide reconciliations of the non-GAAP measures used in this presentation or release to the most comparable GAAP financial measure.

31

Regarding Non-GAAP Financial Measures

32

Regarding Non-GAAP Financial MeasuresFlowers Foods, Inc.

Reconciliation of GAAP to Non-GAAP Measures(000's omitted, except per share data)

For the 16 Week Period Ended

For the 16 Week Period Ended

April 18, 2020 April 20, 2019

Net (loss) income (5,772)$ 65,866$ Income tax (benefit) expense (2,019) 20,199 Interest expense, net 3,314 3,824 Depreciation and amortization 44,663 44,819 EBITDA 40,186 134,708 Other pension cost 143 692 Pension plan settlement and curtailment loss 116,207 - Other pension plan termination costs 133 - Recovery on inferior ingredients - (413) Restructuring and related impairment charges - 718 Project Centennial consulting costs 3,392 - Legal settlements 3,220 150 Executive retirement agreement - 1,331 Canyon acquisition costs - 22 Adjusted EBITDA 163,281$ 137,208$

Sales 1,349,444$ 1,263,895$ Adjusted EBITDA margin 12.1% 10.9%

Reconciliation of Net (Loss) Income to EBITDA and Adjusted EBITDA

33

Regarding Non-GAAP Financial Measures

For the 52 Week Period Ended

For the 52 Week Period Ended

December 31, 2016 December 28, 2019

Net income 163,776$ 164,538$ Income tax expense (benefit) 85,761 47,545 Interest expense, net 14,353 11,097 Depreciation and amortization 140,869 144,228 EBITDA 404,759 367,408 Other pension cost (benefit) (5,638) 2,248 Pension plan settlement loss 6,646 - Project Centennial consulting costs 6,324 784 Acquisition-related costs - 22 Restructuring and related impairment charges - 23,524 Impairment of assets 24,877 - Legal settlements (recovery) 10,500 28,014 Executive retirement agreement - 763 Loss (recovery) on inferior ingredients - (37) Adjusted EBITDA 447,468$ 422,726$

Adjusted EBITDA % change -5.5%

Flowers Foods, Inc.Reconciliation of GAAP to Non-GAAP Measures

(000's omitted)

Reconciliation of Net Income to EBITDA and Adjusted EBITDA

34

Regarding Non-GAAP Financial Measures

35

Regarding Non-GAAP Financial Measures

36

Regarding Non-GAAP Financial Measures

Time Period

Cash Provided by Operating Activities

Purchase of Plant, Property and Equipment Free Cash Flow

FY19 366,952$ 103,685$ 263,267$ FY18 295,893 99,422 196,471 FY17 297,389 75,232 222,157 FY16 356,562 101,727 254,835 FY15 335,674 90,773 244,901 FY14 315,183 83,778 231,405 FY13 270,484 99,181 171,303 FY12 216,880 67,259 149,621 FY11 134,290 79,162 55,128 FY10 306,050 98,404 207,646 FY09 236,009 72,093 163,916 FY08 94,872 86,861 8,011 FY07 214,598 88,125 126,473 FY06 151,276 61,792 89,484 FY05 113,979 58,846 55,133 FY04 123,068 46,029 77,039 FY03 87,989$ 43,618$ 44,371$

* Cash provided by operating activities less purchase of plant, property and equipment.

Reconciliation of Cash Provided by Operating Activities to Free Cash Flow*

Flowers Foods, Inc.Reconciliation of GAAP to Non-GAAP Measures

(000's omitted)