The company admitted that poor safety practices, such as not keeping food at proper temperatures to prevent pathogen growth, sickened customers in Los Angeles and nearby Simi Valley, as well as Boston, Sterling, Virginia, and Powell, Ohio.
The string of outbreaks, which began in August 2015 in Simi Valley, came about two months before an E. coli outbreak at Chipotle spread to multiple states that temporarily closed dozens of restaurants and hurt sales as other food scares emerged. The criminal case was not related to E. coli.
The Newport Beach, California-based company entered into a deferred prosecution agreement that will allow it to avoid conviction by continuing to improve its food safety program, following other rules and paying the record-setting fine for a food safety case, federal prosecutors said.
The company said in a statement that it would continue improving food safety practices that include reducing the number of employees who touch food, testing the quality of raw ingredients and tracing the movement of food supplies to determine where a problem may have occurred.
"This settlement represents an acknowledgment of how seriously Chipotle takes food safety every day and is an opportunity to definitively turn the page on past events,” Brian Niccol, chairman and chief executive officer, said.
Outbreaks of norovirus, which is spread easily by people mishandling food, began in Simi Valley when 234 Chipotle customers and employees became ill. An employee who vomited was sent home, but the illness was not reported internally, as required, and food safety procedures weren't implemented until two days later after multiple customers reported becoming ill.
In December 2015, 141 people reported norovirus type illnesses after visiting a Chipotle restaurant in Boston.
Prosecutors said that outbreak likely began Dec. 3 after an apprentice manager was ordered by a regional manager to continue working after he said he vomited on the job. The incident wasn't reported to company safety officials.
After taking a sick day, the apprentice returned to work and packaged a catering order for the Boston College basketball team. Several players subsequently got sick.
An investigation by the Food and Drug Administration found numerous incidents at other Chipotle restaurants where employees vomited at work, but didn’t go home in violation of the company’s policies, according to court documents. Some former employees said they felt pressured to work when they were sick.
The company apologized for sickening customers in newspaper ads at the end of 2015 and again in 2016. One of its executives acknowledged that people were afraid of their food.
The company then had two norovirus outbreaks in 2017 — one that sickened 135 in Sterling, Virginia, in July and another that made 28 people, including 11 employees, ill in Los Angeles in December.
In July 2018, nearly 650 people got food poisoning after dining at a Chipotle restaurant in Powell, Ohio. The outbreak that caused diarrhea and abdominal pain was tied to bacteria that proliferates when food is not kept at proper temperatures, prosecutors said.
Shares in Chipotle fell nearly 3% to close Tuesday at $786.69.
AP Business Writer Dee-Ann Durbin contributed to this story from Detroit.