Last year's high-profile foodborne illness outbreaks have become a thorn in Chipotle's side. After repeated attempts to win back customers' trust—from free-food deals to serving booze—the company most recently stressed its new, and supposedly improved, food safety measures. But now the chain's founder is admitting to subpar ratings at more than half of his restaurants.

Ells confirmed that only half of the chain's stores get an "A" or "B" grade based on an internal grading system, Fortune reports. Meanwhile, the company's other 1,000 locations—especially ones situated in cities like New York, Philadelphia, and Boston—only earn a "C" grade, in his opinion.

So what, exactly, are the problem areas at these locations? Ells said they have dirty dining rooms, messy soda stations, and slow lines. What's more, the company struggles to extensively train staff since it has seen a much quicker employee turnover rate.

"I'm not satisfied with the rate of recovery and the quality of the restaurant experience," the co-CEO told Fortune. "We are not offering the necessary guest experience. We threw a lot at our employees. We took our eye off the ball on customer service."

Time to step it up again, Chipotle. We're counting on you for our carnitas burrito fix.

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