According to Manager Charles Wright, no one recognized Clinton, who was wearing sunglasses.
The newly-minted presidential candidate ordered a chicken bowl with guacamole, a chicken salad and fruit juice, according to Wright.
"She got great food,” the manager told ABC News. “Everybody loves Chipotle.”
This was just the second Clinton sighting in as many days.
Clinton and her van -- nicknamed “Scooby” after the Scooby Doo Mystery Machine -- are headed for Iowa, where she’ll meet with voters at a local community college.
ABC News' Ben Siegel contributed to this report.