A fuel cell system that controls an anode exhaust gas bleed during power up-transients. The fuel cell system includes a by-pass valve that allows compressor air to by-pass the fuel cell stack and be directly emitted into the cathode exhaust gas stream. The system detects a power up-transient by monitoring the rate of closing of the by-pass valve and the rate of change of an increase in the compressor airflow set-point. If these parameters pass a certain threshold, then the system determines that a power up-transient is occurring, and prevents an anode exhaust gas bleed for a predetermined period of time. If cathode pulsing is occurring where power up-transients come one after another, then the system will continuously reset the time period for preventing the anode exhaust gas bleed until a second time limit is reached, where the bleed is then forced.