Exhibit 99.1

Company Press Release

FLOWERS FOODS, INC. REPORTS FIRST QUARTER 2017 RESULTS

THOMASVILLE, Ga. – Flowers Foods, Inc. (NYSE: FLO), producer of Nature’s Own, Wonder, Tastykake, Dave’s Killer Bread, and other bakery foods, today reported financial results for the company’s 16-week first quarter ended April 22, 2017.

First Quarter Summary:

Compared to the prior year first quarter where applicable

CEO’s Remarks

“Our competitive position remains solid as we navigate a difficult marketplace, said Allen Shiver, Flowers Foods president and CEO. “During the first quarter, with Dave’s Killer Bread, Nature’s Own, and Wonder, we gained share in our key segments of the bread category. We also delivered lower production costs as a percentage of sales, the result of investments in capacity and improved manufacturing efficiencies. In early May, we launched four organic breakfast items to expand offerings under the DKB brand.”

Mr. Shiver continued, “Our top priority is to create value for our shareholders by driving sustainable, profitable sales growth, while improving our operational efficiency. This priority is the focus of Project Centennial. We are on track with our work to streamline the brand assortment, reduce costs for purchased goods and services, and enable independent distributors. Earlier this month, we announced plans to change our organizational structure to support greater brand growth, accountability, operational efficiency, and our long-term strategy. I’m confident these efforts, and the others outlined under Project Centennial, will deliver value to shareholders in line with our long-term goals.”

Updated Guidance for Fiscal 2017:

Matters Affecting Comparability:

In first quarter 2017, the company recorded Project Centennial consulting costs of $15.4 million, a gain on the divestiture of the non-core mix manufacturing business of $28.9 million, net lease termination costs of $0.6 million, and a legal settlement of $0.25 million.

Reconciliation of Earnings per Share to Adjusted Earnings per Share

The Project Centennial consulting costs and the legal settlement are reflected in the selling, distribution and administrative (SD&A) expenses line item of the income statement. Net lease termination costs consist of $1.3 million of lease termination gain recognized in the SD&A expense line item and $1.8 million of lease termination cost recognized in the depreciation and amortization (D&A) line item of the income statement.

Project Centennial Recap

During the first quarter, the company made progress on growth and cost reduction initiatives under Project Centennial, including:

As previously announced on May 3, 2017, the company is being reorganized to emphasize brand growth and innovation, drive enhanced accountability, focus on margin expansion, and strengthen its long-term strategy. The new organizational structure establishes two business units – Fresh Bakery and Snacking/Specialty – and realigns key leadership roles. The company will transition to the new structure over the next several months with full implementation expected during fiscal 2018. Until that time, the company will continue to report results based on its Direct-Store-Delivery (DSD) and Warehouse Delivery segments.

Consolidated First Quarter 2017 Summary

Compared to the prior year first quarter where applicable

Overall softness in the fresh bread category, a competitive marketplace, and the divestiture of the mix manufacturing business resulted in the consolidated sales decline, partially offset by increased sales of the DKB branded products. The national rollout of the DKB brand on Flowers’ DSD network occurred at the beginning of the second quarter of fiscal 2016 resulting in significant sales growth of the brand, year over year.

On a consolidated basis, branded retail sales decreased 1.0% to $693.6 million, store branded retail sales increased 0.5% to $172.0 million, while non-retail and other sales decreased 3.2% to $322.0 million. The decrease in the branded retail category resulted from price/mix declines in soft variety bread and volume declines in cake and other branded retail products, somewhat offset by increased sales of organic bread. The increase in store branded retail sales was mostly attributable to volume increases for variety bread and buns and rolls, partially offset by volume decreases for cake. The impact of the mix manufacturing business divestiture, as well as decreases in volume, resulted in the decline in the non-retail and other category, which includes contract manufacturing, vending and foodservice.

DSD Segment Summary

Compared to the prior year first quarter where applicable

DSD segment branded retail sales increased 0.6% to $646.1 million, store branded retail sales increased 3.4% to $137.5 million, while non-retail and other sales decreased 3.5% to $216.2 million. The branded retail category increased due to significant sales growth of the DKB brand through its national rollout in our DSD markets. Partially offsetting this increase were declines in branded soft variety bread on lower pricing/mix and volume declines for other branded retail items. Store branded retail sales increased primarily due to volume gains in variety bread and buns and rolls. Non-retail and other sales decreased primarily due to volume declines, partially offset by positive pricing/mix.

Warehouse Segment Summary

Compared to the prior year first quarter where applicable

Decreased sales of snack cakes and Alpine Valley branded organic breads, and the impact of the mix manufacturing business divestiture resulted in the sales decrease in the Warehouse segment. Warehouse segment branded retail sales declined 18.6% to $47.5 million, store branded retail sales decreased 9.8% to $34.5 million, while non-retail and other sales decreased 2.7% to $105.8 million. Branded retail sales decreased largely due to volume declines in cake and organic bread. During the second quarter of fiscal 2016, the Warehouse segment’s Mesa, Ariz. bakery significantly increased production of DKB products for the DSD segment. These intercompany sales are not included in the amounts above, but are included in the DSD segment. Higher promotional activity in the prior year quarter, and increased competition in the current year, negatively impacted branded cake sales. Store branded retail sales decreased mainly due to volume decreases in cake. The decrease in non-retail and other sales, which includes contract manufacturing, vending and foodservice, was due primarily to the mix manufacturing business divestiture, partially offset by volume gains in foodservice sales.

Unallocated Corporate Expense Summary

Note: Comparisons are to consolidated sales

Cash Flow, Dividends, Share Repurchases, and Capital Allocation

In the first quarter of fiscal 2017, cash flow from operating activities was $76.0 million, capital expenditures were $17.5 million, and dividends paid were $33.9 million. During the quarter, the company made net payments on debt borrowings of $64.0 million. Net proceeds from the sale of the mix business were $41.2 million.

In the first quarter 2017, the company repurchased 0.1 million shares of its common stock in connection with the vesting of performance share awards. There are 6.7 million shares remaining on the company’s current share repurchase authorization. As in the past, the company expects to continue to make opportunistic share repurchases under this authorization.

Conference Call

Flowers Foods will hold a conference call to discuss its first quarter 2017 earnings at 8:30 a.m. (Eastern) on May 18, 2017. The call can be accessed by clicking on the webcast link on flowersfoods.com. The call also will be archived on the company’s website.

About Flowers Foods

Headquartered in Thomasville, Ga., Flowers Foods, Inc. (NYSE: FLO) is one of the largest producers of fresh packaged bakery foods in the United States with 2016 sales of $3.9 billion. Flowers operates bakeries across the country that produce a wide range of bakery products. Among the company’s top brands are Nature’s Own, Wonder, Tastykake, and Dave’s Killer Bread. Learn more at www.flowersfoods.com.

Investor Contact: J.T. Rieck (229) 227-2253

Media Contact: Paul Baltzer (229) 227-2380

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) 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; and (m) 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.

Information 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 by segment, adjusted EPS, 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 from continuing operations before interest, income taxes, depreciation, amortization and income attributable to non-controlling interest. 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 depending upon accounting methods and non-operating factors (such as historical cost). 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, adjusted net income, adjusted operating income by segment, and adjusted net income per diluted share, respectively, excluding the impact of asset impairment charges, acquisition-related costs, and pension plan settlements. 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.

Net 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 according to 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.

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Consolidated Statement of Income

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Segment Reporting

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Condensed Consolidated Balance Sheet

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Condensed Consolidated Statement of Cash Flows

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Reconciliation of GAAP to Non-GAAP Measures

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Reconciliation of GAAP to Non-GAAP Measures

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Sales Bridge