A system and method for operating a fuel cell system in a stand-by mode. The method includes determining a power limit value based on fuel cell stack and battery power optimization, where if a system power request falls below the power limit value the system will enter the stand-by mode. The system first enters a dynamic stand-by mode where the fuel cell stack is turned off and a compressor providing cathode air to the cathode side of the stack is operated at an idle speed. The method accumulates a compressor power value identifying how much energy has been consumed by operating the compressor at the idle speed during the dynamic stand-by mode, and then switches to a static stand-by mode where the compressor is turned off when the accumulated compressor power value reaches a compressor restart energy value that identifies how much energy it takes to start the compressor.