Chipotle has run short of beef from time to time, and last December it announced that it could not supply all of its restaurants with the pork needed for carnitas after an audit found that one of its suppliers had failed to meet its standards for raising pigs.

That shortage continues, cutting into the company’s sales, and last week it said it probably would not be able to offer carnitas in all of its more than 1,800 restaurants until this fall.

Mr. Ells said he did not expect to run into the same problem with supplies of non-G.M.O. ingredients. “We’re working with our farmers to plan enough of these crops we need to meet our supply,” he said. “With pork, it’s harder because we only need one part of the animal, the shoulder, and the farmer needs to sell the whole animal to make it work.”

Eliminating genetically engineered ingredients is easier for Chipotle, where the entire menu uses just 68 ingredients, including salt and pepper, while one of its competitors uses 81 just to make a burrito. “The vast majority of our ingredients don’t come in a G.M.O. variety, and we use lots of whole, unprocessed foods, so it was easier for us to do,” Mr. Ells said.

More than 90 percent of corn and soy grown in the United States is genetically modified, and Chipotle used soy oil to fry its chips and tortillas. Canola oil comes from rapeseed, another large G.M.O. crop.

Getting rid of genetically engineered corn was easiest. Chipotle’s primary tortilla supplier was already producing non-G.M.O. corn flour in small amounts, and it agreed to increase its production.

But one oil can’t simply replace another. Different oils have different smoking temperatures. They impart different flavors and have varying viscosity.