Mr. Ells said the company would announce changes to the board shortly.

Mr. Moran, who was appointed to his position in 2009, was known as somewhat of a taskmaster when it came to overseeing employees. Before he was a co-chief executive, he was the chief operating officer.

Last week, Chipotle executives said that in part because of an extensive new food safety program the company instituted over the last year, the amount of time it took customers to get through the assembly line as their meal was made had increased. Spot checks by executives and the company’s auditing team found used napkins left on tables, smudged windows and doors, and messy condiment stations. Some customers using the Chipotle app to order were told their meal would not be ready for 45 minutes to an hour.

Such issues largely came under Mr. Moran’s supervision, but will now fall to Mr. Ells, a self-described perfectionist who founded Chipotle in 1993 with a loan from his father.

“Prior to the crisis, we would have maybe six, seven or eight changes to our operational protocols a year,” Mr. Ells said. “Post-crisis, we’ve introduced dozens and dozens of them, and that’s a lot to handle.”

He said that while employees had received top marks from internal auditors for embracing those changes, many of which were related to improving food safety, that may have caused lapses in other areas, including customer experience.

“We have a terrific team, and our managers are terrific managers,” Mr. Ells said, “but we have made it too complicated for them and too complicated in a way that they just can’t do an excellent job in many cases when it comes to the customer experience.” He said any changes would not come at the expense of food safety.

Mr. Ells said he planned to change the incentives for employees who excel. Chipotle is already one of the handful of large restaurant chains that pays starting employees above minimum wage, and it offers benefits like paid vacation, sick leave and tuition reimbursement.