Exhibit 99.1

Company Press Release

FLOWERS FOODS, INC. REPORTS THIRD QUARTER 2016 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 12-week third quarter ended October 8, 2016.

Summary:

Compared to the prior year third quarter where applicable

CEO’s Remarks

“While we are pleased with the performance of Dave’s Killer Bread, which continues to gain share as America’s #1 organic bread brand, our results in the third quarter were affected by challenging category dynamics and elevated marketing and legal costs,” Allen Shiver, Flowers Foods president and CEO, said. “We remain acutely focused on driving growth and increasing efficiencies, including our Project Centennial efforts. The initial diagnostic phase is complete, and we are now finalizing our plans to implement strategies intended to grow sales and improve margins. Today, Flowers is a strong company with a team dedicated to excellence. Looking ahead, we are confident we are taking the right steps to build on our strong foundation and enhance shareholder value over the long term.”

Project Centennial Update

During the quarter, Flowers progressed towards the completion of the first phase of Project Centennial, which included a comprehensive diagnostic evaluation of opportunities to drive growth, reduce costs, and make investments intended to strengthen the company’s competitive position and improve margins over the long term.

In mid-October, Flowers began the second phase which entails formulating and executing new strategies to capture growth opportunities. To fund these initiatives, the company is currently finalizing the specific actions necessary to achieve savings through identified operational improvements that include further use of the company’s shared services capabilities, network optimization, and better leveraging the company’s expenditures on goods and services. The company anticipates finalizing the implementation plans in early 2017, and expects to provide additional details on Project Centennial when Flowers fiscal 2016 results are released in early February.

Consolidated Third Quarter 2016 Results Commentary

Consolidated sales for the quarter were $918.8 million, an increase of 3.8% compared to the prior year third quarter. Of the consolidated sales increase, acquisitions until cycled contributed 4.4%, pricing/mix increased 0.3%, and volume decreased 0.9%.

Diluted EPS in the third quarter 2016 was $0.19, a decrease of $0.02, or 9.5%, when compared to third quarter 2015 diluted EPS of $0.21. Excluding settlement costs associated with our pension de-risking strategy, a legal settlement charge discussed below, and additional interest expense resulting from the payoff of the term loans described below, adjusted diluted EPS was $0.21, a decrease of $0.02 per share, or 8.7%, when compared to third quarter 2015 adjusted diluted EPS of $0.23. In the third quarter of 2015, adjusted diluted EPS excluded acquisition-related costs and facility closure costs of $0.02 per share.

Subsequent to quarter end, on November 8, 2016, Flowers Foods’ subsidiary, Lepage Bakeries, reached an agreement to settle a class-action lawsuit in Connecticut for $1.25 million, including attorneys’ fees and certain non-economic terms which are intended to strengthen and enhance the independent contractor model. This agreement, which includes 49 territories, is subject to court approval.

During the third quarter, the company issued $400 million of senior notes due 2026 and bearing a fixed interest rate of 3.5%. Proceeds from the notes were used to repay debt outstanding under our existing term loan facilities and a portion of our accounts receivable securitization facility. In connection with the payoff of the term loan facilities, debt issuance costs of $1.9 million associated with the term loan facilities were recorded as interest expense in the current quarter. Net interest expense, excluding the additional interest expense resulting from the payoff of the term loams described above, increased when compared to the prior year third quarter due to higher borrowings resulting from investments in DKB and Alpine in fiscal 2015.

Net income in the third quarter 2016 was $40.2 million, a decrease of 8.2% when compared to the third quarter 2015. The decline in net income was driven primarily by higher workforce-related costs, marketing expenses, legal costs, depreciation and amortization, pension plan settlement cost, legal settlement charge, and net interest expense, partially offset by lower income taxes and the absence of facility closure costs and acquisition-related costs.

Excluding settlement costs associated with our pension de-risking strategy, the legal settlement charge, and additional interest expense resulting from the payoff of the term loans described above, adjusted net income was $43.3 million.

Consolidated adjusted EBITDA for the quarter was $101.7 million, a decrease of 3.0% when compared to the third quarter 2015. Adjusted EBITDA margin was 11.1%, a decrease of 70 basis points when compared to the prior year third quarter. As a percentage of sales, declines in input costs (ingredients, packaging, and utilities) and distributor distribution fees were offset primarily by increases in workforce-related costs, marketing expenses (primarily due to the rollout of DKB) and certain legal costs. As anticipated, purchases of co-manufactured product have begun to decline as a percentage of sales, due to the additional organic production capacity provided by our Tuscaloosa, Ala. bakery, which began producing organic bread at the beginning of the second quarter 2016.

Cash Flow

During the quarter, cash flow from operating activities was $91.2 million, capital expenditures were $25.7 million, and dividends paid were $33.2 million. Also during the quarter, the company issued $400 million of senior notes. With the net proceeds from the issuance, combined with cash generated from operations, the company made net payments on debt borrowings of $46.6 million.

DSD Segment Third Quarter Results Commentary

Direct-Store-Delivery (DSD) segment sales for the quarter were $768.9 million, an increase of 3.0% compared to the prior year third quarter. Of this increase, the DKB acquisition contributed 4.0% until cycled, volume decreased 2.1%, and pricing/mix increased 1.1%. Excluding the DKB acquisition until cycled, positive price/mix in the branded retail category was more than offset by volume declines in the category driven by the competitive marketplace. Branded soft variety and specialty loaf breads, as well as branded cake, experienced the largest declines, partially offset by growth in branded buns and rolls and store brand loaf breads. Non-retail and other sales decreased primarily due to volume declines.

DSD segment operating income for the quarter was $66.3 million, a decrease of 10.1% compared to the prior year third quarter. Operating margin for the DSD segment was 8.6% in the third quarter, as compared to 9.9% in the prior year quarter. Items negatively impacting DSD segment operating income and adjusted EBITDA are described below. Also negatively impacting DSD segment operating income was higher depreciation and amortization expense and the legal settlement charge. In the third quarter of 2015, DSD segment operating income was negatively impacted by facility closure costs of approximately $0.7 million.

DSD segment adjusted EBITDA, excluding the legal settlement discussed above, for the quarter was $95.4 million, a decrease of 5.0% compared to the prior year third quarter, adjusted for facility closure costs. Adjusted EBITDA margin for the DSD segment was 12.4% in the third quarter, as compared to 13.5% in the prior year quarter. As a percentage of sales, declines in input costs and distributor distribution fees were more than offset by higher workforce-related, legal, and marketing costs. Outside purchases of DKB products have decreased due to the additional capacity provided by the Tuscaloosa bakery conversion, as well as the Alpine bakery in the Warehouse segment.

Warehouse Segment Third Quarter Results Commentary

Warehouse segment sales for the quarter were $149.9 million, an increase of 7.8% compared to the prior year third quarter. Of this increase, pricing/mix decreased 1.3%, volume increased 2.8%, and the Alpine acquisition contributed 6.3%. Excluding the Alpine acquisition, volume growth of branded retail bakery/deli items, contract manufacturing, and foodservice (driven by new foodservice products for certain customers), more than offset volume declines of branded retail items and pricing/mix declines largely due to lower foodservice and contract manufacturing pricing/mix.

Warehouse segment operating income for the quarter was $12.3 million, an increase of 8.1% compared to the prior year third quarter. Operating margin for the Warehouse segment was 8.2% in the third quarter, the same as the prior year quarter. Higher depreciation and amortization expense negatively impacted Warehouse segment operating income. Lower input costs and increased sales positively impacted Warehouse segment operating income and EBITDA.

Warehouse segment EBITDA for the quarter was $16.9 million, an increase of 13.1% compared to the prior year third quarter. EBITDA margin for the Warehouse segment was 11.3% in the third quarter, as compared to 10.7% in the prior year quarter. As a percentage of sales, increases in workforce-related and marketing costs were more than offset by lower input costs and increased sales volumes.

Dividends and Share Repurchases

Year-to-date, the company has repurchased approximately 6.9 million shares. Currently, there are 6.8 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.

Since the beginning of fiscal 2016, through both dividends and share repurchases, the company has returned $224.1 million to shareholders.

Conference Call

Flowers Foods will broadcast its third quarter 2016 earnings conference call on www.flowersfoods.com at 8:30 a.m. (Eastern) on November 10, 2016. The call can be accessed by clicking on the webcast link on the home page. 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 2015 sales of $3.8 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) consolidation within the baking industry and related industries; (j) 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; (k) increasing legal complexity and legal proceedings that we are or may become subject to; and (l) 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 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 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 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 company may from time-to-time discuss SD&A adjusted for items that are not continuing in nature. 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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Sales Bridge