The typical Chipotle General Manager salary is $49,883. General Manager salaries at Chipotle can range from $33,692 - $70,207. This estimate is based upon 150 Chipotle General Manager salary report(s) provided by employees or estimated based upon statistical methods. When factoring in bonuses and additional compensation, a General Manager at Chipotle can expect to make an average total pay of $53,304 . See all General Manager salaries to learn how this stacks up in the market.