We wrote last month about the challenges facing Chipotle, a favorite restaurant of many Americans. Now another industry leader is facing similar challenges. Whole Foods Market Inc. has had a tough few years. Most recently, the Food and Drug Administration, in a series of crackdowns, told the industry’s leading company to clean up its act.

On June 8, the FDA issued a warning letter to the co-CEOs of Whole Foods, John Mackey and Walter Robb. The letter stated that the health food chain had 15 days to address the “serious violations” the FDA found while inspecting the company’s Massachusetts ready-to-eat food preparation plant in February. The FDA emphasized Whole Foods’ failure to prepare and store foods in a way that reduced the potential for organism growth and contamination. It cited evidence of listeria, condensation from pipes falling directly on food, and the accidental spraying of sanitizer on salad greens. The FDA has not pointed to any evidence of harm, but it expressed serious concerns regarding the state of the facility, as the pre-prepared food “may have been contaminated with filth or rendered injurious to health.”

According to Whole Foods’ executive vice president, Ken Meyer, the June warning letter came as a surprise. The company insists that it has maintained close contact with the FDA since it received its first warning letter in February for similar violations, and that it is surprised the most recent warning letter did not reflect any of the “thorough and tangible” steps Whole Foods has taken to resolve the FDA’s concerns. The FDA appears to be unsatisfied with Whole Foods’ performance, labeling its steps “inadequate,” because the company did not provide documentation of corrections or establish forward-looking compliance procedures.

Whole Foods’ time to respond to the June warning letter has passed, and it is unclear what steps the company has taken to resolve the FDA’s concerns. What is clear, however, is that the FDA is paying close attention to even the largest and most well-respected food companies.

Rachael V. Mozelewski is the author of this article.