NEW YORK — After an E. coli outbreak that sickened more than 50 people, Chipotle is tweaking its cooking methods.

Onions will be dipped in boiling water to kill germs before they’re chopped. Raw chicken will be marinated in re-sealable plastic bags, rather than in bowls. Cilantro will be added to freshly cooked rice so the heat gets rid of microbes in the garnish.

“When you’re given a project like this, you look at the universe of hazards,” sad Mansour Samadpour, CEO of IEH Laboratories, which was hired by Chipotle to tighten its procedures.

The changes mark a dramatic turn in fortunes for Chipotle, which has surged in popularity by touting its “Food With Integrity” slogan. As it expanded to more than 1,900 locations, the company also sought to draw a distinction between itself and other fast-food chains that executives said use “chemical additives” and “cheap artificial ingredients.”

Now, Chipotle Mexican Grill may be suffering from traits that helped define it. In its annual report in February, the company noted it may be at a higher risk for foodborne illnesses because of its use of “fresh produce and meats rather than frozen,” and its traditional cooking methods,” rather than “automation.”

The warning started coming to life this summer when the chain was tied to foodborne illnesses in California and Minnesota.

Then, at the end of October, E. coli cases were reported in Oregon and Washington, prompting the company to shut down 43 restaurants in those states. YouGov Brand Index said customer perceptions about Chipotle sank to their lowest level since it began tracking the company in 2007.