Natasha Velez, 27, filed a lawsuit against the fast-casual chain in Manhattan Federal Court, the New York Daily News reports.
Velez claims that an attack by an ex-boyfriend left her with a broken finger and doctors insisted she take two weeks off work.
When she returned to the Upper East Side for her Chipotle shift, the manager allegedly told her she was fired because of her personal life, Velez told the Daily News.
Velez, who has a young daughter, says she has faced financial hardship since losing her job. Her lawsuit seeks her job, wages, and unspecified damages.
A representative for Chipotle said the company does not comment on pending litigation.