Exhibit 99.1

Company Press Release

Flowers Foods, Inc. Reports Fourth Quarter and Full Year 2015 Results

Record Adjusted EPS of $0.92 per share in Fiscal 2015

Provides 2016 Guidance

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 fourth quarter and year ended January 2, 2016 and provided guidance for fiscal 2016.

Reported results reflect that the fourth quarter of fiscal 2014 was a 13-week quarter and fiscal 2014 was a 53-week year. The fourth quarter of fiscal 2015 was a 12-week quarter and fiscal 2015 was a 52-week year. The company’s fiscal 2016 will also be a 52-week year.

Note: Summary information below has been adjusted for the following items that affect comparability to prior periods: asset impairments, divestitures, pension plan settlement loss, and acquisition-related costs. Please see non-GAAP reconciliations in the tables at the end of this release.

Fiscal 2015 Summary:

Compared to the prior fiscal year -

Fourth Quarter Summary:

Compared to the prior year fourth quarter -

For 52-week Fiscal 2016, the Company Expects:

President and CEO Allen Shiver said, “We are not satisfied with our performance in the fourth quarter. Even so, for the full year we delivered record adjusted EPS and we took important steps to position Flowers for opportunities in 2016 and beyond.

“While we continued to make significant progress on our strategic initiatives, our earnings in the fourth quarter were impacted by sales that were below plan. In line with channel data for the total store, the pace of Flowers’ retail sales in the fourth quarter slowed relative to trends we observed in the first three quarters. Due to the lower than anticipated sales, our earnings for the quarter were negatively impacted by approximately $0.03 per share. Additionally, certain costs originally planned for the first quarter of 2016 were incurred in the fourth quarter of 2015, impacting EPS by $0.01.

“It would be a mistake not to recognize the team’s accomplishments during the year on several initiatives integral to Flowers’ long-term strategy to grow in underdeveloped categories and geographies.

“First, with our acquisitions of Dave’s Killer Bread and Alpine Valley Bread, we grew Flowers’ share in the fast-growing organic segment of the specialty premium category, extended our geographic reach, and broadened our retailer relationships.

“Second, our investments in growth, including the successful opening of our bakery in Lenexa, Kan., enhanced our ability to serve the Midwest with Flowers’ strong brands and position us to sustain our expansion market growth.

“Third, to keep up with the ever-changing consumer landscape, we have not only offered new items, such as our Cobblestone Bread Company “Right Sized” breads, but also carefully evaluated our product assortment, improving our merchandising and promotional strategies. We remain focused on trade promotion effectiveness and efficiency,” Shiver said.

In fiscal 2015, Flowers generated operating cash flow of $327.3 million, which we used to make capital expenditures of $93.8 million, make debt repayments of $143.2 million (excluding withdrawals for recently completed acquisitions), increase our dividend per share by 17.0% year-over-year, and repurchase 0.3 million shares for $6.9 million.

Shiver concluded, “While we did not meet our fourth quarter objectives, fiscal 2015 was a strong year for Flowers. Looking ahead, recently completed acquisitions, which are a core part of our growth strategy, are expected to contribute between 5.2% and 5.7% to sales growth in 2016. And with our strong brands we are working to grow share in expansion markets while remaining a low-cost producer. The team remains keenly focused on executing our growth strategies and delivering shareholder value.”

Segment Results for the Quarter and Fiscal Year

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

DSD Segment Fourth Quarter Results Commentary

Of the total DSD segment sales decrease during the quarter, pricing/mix was neutral, volume decreased 0.3%, the DKB acquisition contributed 3.8%, and the impact of the extra week in the prior year resulted in a negative impact of 7.2%. Excluding the effect of acquisitions and the extra week, branded retail sales were up slightly, with volume increases in white and soft variety breads, driven by Nature’s Own and Wonder, mostly offset by lower sales of sandwich buns and rolls, and sandwich rounds. 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, excluding the impact of the extra week.

Adjusted EBITDA margin for the DSD segment decreased as a percentage of sales due to higher workforce-related costs and lower efficiencies (due to below-plan sales), as well as increases in outside purchases of product, primarily due to capacity constraints at DKB.

Warehouse Segment Fourth Quarter Results Commentary

Of the Warehouse segment’s sales increase, pricing/mix decreased 0.6%, volume increased 5.6%, the Alpine acquisition contributed 8.8%, and the impact of the extra week in the prior year resulted in a negative impact of 7.6%. Excluding the effect of the acquisition and the extra week, the slight increase in branded retail sales was primarily due to a positive shift in mix within branded snack cake and volume gains in bakery deli. Excluding the extra week, the improvement in store branded retail sales was primarily the result of higher store branded cake sales. The significant increase in non-retail and other sales was driven by new foodservice products.

EBITDA margin for the Warehouse segment increased as a percentage of sales, primarily due to ingredient cost decreases, partially offset by higher workforce-related costs and reduced efficiencies (due to below-plan sales).

Consolidated Fourth Quarter Results Commentary

As compared to the prior year fourth quarter, consolidated adjusted EBITDA decreased by 6.7%. Adjusted unallocated corporate expenses were elevated during the quarter, primarily due to higher legal expenses, and lower pension income – partially offset by lower stock-based compensation expense.

Depreciation and amortization increased due primarily to the DKB and Alpine acquisitions. Interest expense increased primarily due to higher average debt balances driven by recent acquisitions. Interest income decreased primarily due to lower average notes receivable balances. Income tax expense as a percentage of pre-tax income increased primarily as a result of the release of uncertain tax positions in the prior year.

Cash Flow

During the quarter, cash flow from operating activities was $46.7 million, capital expenditures were $32.5 million, cash paid for Alpine, net of cash acquired, was $109.4 million, and dividends paid were $30.8 million.

Dividends 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. During fiscal 2015, the company repurchased 0.3 million shares at an average price of $21.54 per share. There are 13.7 million shares remaining on the company’s current share repurchase authorization.

Conference Call

Flowers Foods will broadcast its fourth quarter and full year 2015 earnings conference call over the Internet at 8:00 a.m. (Eastern) on February 11, 2016. 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 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, 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, 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, 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, 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, and adjusted EBITDA, a reconciliation of adjusted EBITDA to cash flow from operations, and a reconciliation of net income per diluted common share to adjusted net income per diluted common share.

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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