A fuel cell system having an adaptable compressor map and method for optimizing the adaptable compressor map is provided. The method includes the steps of establishing an initial operating setpoint for an air compressor based on the adaptable compressor map; monitoring a surge indicator; adjusting the adaptable compressor map based on the monitored surge indicator; determining a desired operating setpoint based on the adjusted adaptable compressor map; and establishing an adapted operating setpoint for the air compressor based on the adaptable compressor map following the adjustment thereof. The steps are repeated until the adaptable compressor map for the air compressor is optimized.