Exhibit 99.1

Flowers Foods, Inc. Announces Results for the Third Quarter 2015

THOMASVILLE, Ga. – Flowers Foods, Inc. (NYSE: FLO), producer of Nature’s Own, Wonder, Tastykake, and other bakery foods, today reported financial results for the company’s 12-week third quarter ended October 10, 2015.

Third Quarter 2015 Summary Financial Results

Compared to prior year third quarter

Third Quarter Highlights

Fiscal 2015 Outlook - Updated

Segment Results for the Quarter

Note: Amounts and percentages may not compute due to rounding.

Executive Commentary:

Allen L. Shiver, president and chief executive officer, said, “It is an exciting time at Flowers. The team is working hard to capture the potential of our strong brands and geographic reach. Our recently acquired organic bread brands – Dave’s Killer Bread and Alpine Valley Bread – are on-trend with changing consumer preferences and provide Flowers with additional growth opportunities through expanded distribution. We recognize the quality and values these brands represent, and a key focus as we bring the Flowers, DKB, and Alpine Valley teams together will be to maintain the integrity of their great brands.

“Sales growth this quarter, excluding the impact of DKB, was driven by continued gains in our expansion markets, strong performance from our branded bread and rolls, and foodservice volume gains. Continuing a trend from the second quarter, our branded cake sales also posted year-over-year growth. Leveraging our consolidated sales growth, we grew adjusted EBITDA 6.1%.

Shiver continued, “This year, we’ve opened a new bakery in Lenexa, Kan., introduced new products under our existing brands, and completed acquisitions to support future growth. Considering all factors, it was necessary to narrow our outlook for 2015. Even so, as we look ahead to 2016, we are committed to capitalizing on the opportunities provided by our strategic acquisitions and building on our strong foundation.”

DSD Segment Commentary

Of the total DSD segment sales increase, pricing/mix increased 0.2%, volume increased 2.9%, and the acquisition of Dave’s Killer Bread contributed an additional 1.4%. Branded retail sales were strong, primarily due to volume increases in white and soft variety breads and the DKB acquisition contribution. New product introductions and further expansion in our DSD markets drove increased sales of Tastykake products. Driven primarily by the foodservice business, the non-retail and other category posted solid growth.

Adjusted EBITDA margin for the DSD segment increased as a percentage of sales due to lower ingredient costs and cost-saving initiatives, partially offset by higher workforce-related costs and increases in outside purchases of product, primarily due to capacity constraints at DKB.

Warehouse Segment Commentary

Of the Warehouse segment’s sales increase, pricing/mix increased 0.6%, and volume increased 5.5%. The increase in branded retail sales was primarily due to volume gains in bakery deli and mix shift within branded snack cake. The improvement in store branded retail sales was primarily the result of higher store branded cake sales. The increase in non-retail and other sales was driven by new foodservice products.

EBITDA margin for the Warehouse segment decreased as a percentage of sales, primarily due to higher employee incentive costs and reduced efficiencies.

Consolidated Results Commentary

As compared to the prior year third quarter, consolidated adjusted EBITDA increased by 6.1%. Adjusted unallocated corporate expenses were elevated during the quarter, primarily due to higher consulting and legal expenses, and lower pension income – partially offset by lower stock-based compensation expense.

Interest expense declined due to lower average outstanding debt balances, while a higher average notes receivable balance drove an increase in interest income. Income tax expense as a percentage of pre-tax income increased primarily as a result of certain non-deductible acquisition-related costs.

Cash Flow

During the quarter, cash flow from operating activities was $64.6 million, capital expenditures were $20.7 million, cash paid for DKB, net of cash acquired, was $280.8 million, and dividends paid were $30.5 million.

Dividend and Share Repurchases

The board of directors will review the dividend at its next regularly scheduled meeting. Any action taken will be announced following that meeting.

During the quarter, the company made no share repurchases. There are 13.7 million shares remaining on the company’s current share repurchase authorization.

Conference Call

Flowers Foods will broadcast its third quarter 2015 earnings conference call over the Internet at 8:30 a.m. (Eastern) on November 12, 2015. The call will be broadcast live on www.flowersfoods.com, and 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 2014 sales of $3.75 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, and Tastykake. Learn more at www.flowersfoods.com.

Investor Contact: J.T. Rieck (229) 227-2348; 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, and (k) 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, adjusted EBITDA margin, adjusted net income, and adjusted net income per diluted common share.

EBITDA is used as the primary performance measure in the company’s 2014 Omnibus Equity and Incentive Compensation Plan. 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. 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.

Adjusted EBITDA, adjusted EBITDA margin, adjusted net income, and adjusted net income per diluted common share exclude additional costs that we consider important to present to investors. These include, but are not limited to, the costs of closing a plant or costs associated with acquisition-related activities. We believe that financial information excluding certain transactions not considered to be part of the ongoing business improves the comparability of earnings results. We believe investors will be able to better understand our earnings results if these transactions are excluded from the results. These non-GAAP financial measures are measures of performance not defined by accounting principles generally accepted in the United States and should be considered in addition to, not in lieu of, GAAP reported measures. None of these non-GAAP measures should 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. Our method of calculating EBITDA, adjusted EBITDA, adjusted EBITDA margin, adjusted net income, and adjusted net income per diluted common share, may differ from the methods used by other companies, and, accordingly, may not be comparable to similarly titled measures used by other companies.

The reconciliations attached provide a reconciliation of our net income, the most comparable GAAP financial measure to EBITDA, adjusted EBITDA and adjusted net income, a reconciliation of adjusted EBITDA to cash flow from operations, a reconciliation of net income per diluted common share to adjusted net income per diluted common share and reconciliations of operating income (EBIT) to adjusted EBITDA by segment.

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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