But both Gray and Bastianich said that Chipotle will stick with its "fundamental DNA" of fresh food — and long term, that's a good thing. Indeed, Gray's research has shown that attention to food safety can keep compliance from fading to the background among priorities like cost, delivery and animal welfare (at least for a while).
Ells reiterated that at the Bernstein Consumer Summit.
"In regards to local farms, there will be robust testing procedures that will need to be in place for all of our suppliers, whether they're large or small," he said. "Some of the smaller suppliers might have a hard time implementing these robust testing procedures initially. We'll help them. Not all will be on board, for sure, but we think that most will."
And as Chipotle searches for the right balance of of costly testing and small suppliers, regulators do too.
Local foods were spotlighted in a 2015 USDA report as a priority for goals like "enhancing the rural economy, the environment, food access and nutrition, informing consumer demand, and strengthening agricultural producers and markets." But practices such as the prolific use of manure at local farms has presented challenges in properly implementing The Food Safety Modernization Act, the USDA report said.
"Currently, food safety in produce is a hodgepodge of decisions by individuals, grower organizations, buyers and governments that can vary by farm size, commodity, region and country," the researchers wrote.
"Obviously it's a super-ambitious idea," Bastianich said. "[Chipotle is] an incredible company, [co-CEO Steve Ells] is an incredible guy to think about all this. And this is a bump in the road ... unfortunately, it's going to hurt."
Chipotle did not immediately respond to a request for comment.
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— CNBC's Katie Little contributed to this report.