A method of shutting down operation of a fuel cell system is disclosed, comprising a fuel cell stack, the method comprising the sequential steps of: i) ceasing a supply of fuel to the fuel cell stack; ii) closing a shut-off valve on an exhaust line in fluid communication with a cathode system of the fuel cell system, the cathode system comprising a cathode fluid flow path passing through the fuel cell stack; iii) pressurizing the cathode system with an air compressor in fluid communication with a cathode air inlet port in the fuel cell stack; and iv) ejecting water from the cathode flow path.