John Mackey, CEO of Whole Foods Market

Whole Foods reported quarterly earnings and revenue that met analysts' expectations on Wednesday, but a key industry metric disappointed Wall Street.

The company posted fiscal third-quarter earnings at 37 cents per share, which met analysts estimates, down from 43 cents in the year-ago quarter. Revenue for the quarter came in at $3.7 billion, roughly in line with analysts' estimates of $3.73 billion. This was higher than last year's comparable figure of $3.63 billion.