A fuel cell system that employs a procedure for delaying an air purge of a fuel cell stack at system shut-down until the temperature of the stack is reduced below a predetermined temperature. The fuel cell stack includes an anode side, a cathode side, an anode input, a cathode input and an anode exhaust. The system includes a temperature sensor for monitoring the temperature of a cooling fluid flowing through the stack. The anode side of the fuel cell stack is purged at the stack shut-down by directing air from the cathode input line to the anode input line after the temperature of the cooling fluid is reduced to a predetermined temperature.