Whole Foods earnings: 46 cents per share, vs expected EPS of 40 cents

Whole Foods reported quarterly earnings and revenue that beat analysts' expectations on Wednesday.

The company said it saw fiscal year first-quarter earnings of 46 cents per share on $4.83 billion in revenue. Analysts had expected Whole Foods to report earnings of about 40 cents share on $4.81 billion in revenue, according to a consensus estimate from Thomson Reuters.

Shares of the company briefly rose 6 percent in after-hour trading. Year-over-year the stock is down more than 46 percent.

A customer shops for produce at a Whole Foods Market in San Francisco.
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A customer shops for produce at a Whole Foods Market in San Francisco.

Revenue for the quarter was up about 3 percent from the $4.67 billion in the year-ago period, the company said.

"We delivered record sales of $4.8 billion this quarter and are pleased with the progress we have made on our nine-point plan outlined in November," Walter Robb, co-chief executive officer of Whole Foods, said in a statement. "We improved our cost structure, stepped up our value efforts, and are excited to announce today the national launch of digital coupons within our mobile app."

Robb expects the company to deliver strong returns to shareholders in the future, as price perceptions improve.

Whole Foods recently came under fire in New York City for overcharging its customers, but the company told CNBC that consumers who choose generic brands or shop for in-season produce, can save money on their groceries.

"As the demand for organics foods rises, the supply has become more plentiful and prices are becoming increasingly competitive," Joe Dickson, quality standards coordinator for Whole Foods Market, told CNBC in a recent interview.

The company said that it opened three new stores in the first-quarter and two in the second-quarter. Six additional stores are slated to open in the near future.

In early November, Whole Foods announced a $1 billion stock buyback program, dividend increase and capital structure plan.

— CNBC's Denise Garcia contributed to this report.