A sign taped to a window read, "Ask our corporate offices why their employees are forced to work in borderline sweatshop conditions," according to the sign.
"Our Penn State restaurant was closed part of the day yesterday when a few employees quit, locking out a majority of others who are enthusiastic to return to work," company spokesman Chris Arnold said in an e-mail.
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Chipotle Mexican Grill runs a chain of more than 1,500 restaurants that have helped put the fast-casual category of restaurants on the food map. Fast-casual dining promises higher quality food without table service.
During an investor call with Wall Street analysts in January, Chipotle co-CEO Monty Moran said average wages were at $9 an hour, and that a move to $10 would have an effect on the company, "but not too significant." That wage range already is higher than $7.25, the current, hourly federal minimum wage. Recent efforts to raise the federal minimum to $10.10 an hour have stalled.
Read MoreChipotle, Starbucks navigate the minimum-wage fray
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