Chipotle Pulls Jalapeños Nationwide After Link to Salmonella Outbreak

Chipotle Mexican Grill removed jalapeños from its restaurants nationwide on Tuesday after the pepper was identified as a possible source of a salmonella outbreak that has sickened at least 110 people in Minnesota — with a separate cluster of 110 cases also identified in Colorado linked to the same bacterial strain.

What Triggered the Removal

The Chipotle jalapeños salmonella outbreak Minnesota 2026 investigation began after Minnesota health officials identified a cluster of Salmonella javiana cases tied to Mexican-style quick-service restaurants. Of the 84 Minnesota patients interviewed as part of the investigation, 75 — or 89% — reported eating at a Chipotle location between June 14 and July 14, with most visits concentrated between June 24 and July 2.

“As part of our established health and safety protocols, upon learning of a potential outbreak, we immediately initiated our ingredient traceability system and were able to identify jalapeños as a potential common ingredient from a common lot,” Chipotle said in a statement. The company said it removed the peppers from every restaurant where the affected lot had been distributed and replaced them with product from different growers.

Outbreak Extends Beyond Chipotle

Health officials stressed that the contaminated jalapeños were distributed to multiple food service retailers across several states — not exclusively to Chipotle. Patients who reported no Chipotle visits said they had eaten at other Mexican-style restaurants. “Based on all the evidence so far, the food that made people sick was served at other restaurants as well,” said Carlota Medus, senior epidemiologist supervisor at the Minnesota Department of Health.

“Given the measures Chipotle put in place, we are not concerned about Chipotle, but it is possible that the outbreak is ongoing if the contaminated food item is being served elsewhere,” Medus added. She also warned the case count is likely to rise, as surveillance systems take time to detect illnesses that occurred weeks earlier.

The FDA confirmed it initiated a traceback investigation of “multiple ingredients” on July 22 following a cluster of cases identified by both state health departments and the CDC. The FDA said it would provide further information “if and when there is an actionable public health update.” Neither the FDA, Minnesota health officials, nor Chipotle has identified the jalapeño supplier or named the other states with suspected cases.

Jalapeños Used in Multiple Chipotle Items

Jalapeños are an ingredient in several Chipotle menu items, including guacamole, pico de gallo, and chili-corn salsa. Chipotle said all affected product has been removed and replaced with peppers from different suppliers at all impacted locations.

Stock Falls Nearly 10% as Food Safety Concerns Mount

Chipotle shares fell approximately 10% Tuesday on the news, reflecting investor sensitivity to food safety issues — both the specific Chipotle history and the broader climate of concern following the ongoing cyclospora outbreak linked to lettuce that has sickened thousands of Americans in 34 states. Although salmonella and cyclospora are different pathogens, the simultaneous outbreaks have weighed on consumer confidence and restaurant and produce demand.

Chipotle was implicated in at least five separate foodborne illness outbreaks between 2015 and 2018. The company subsequently overhauled its food safety program and has been widely considered an industry leader on the issue in recent years.