A method for purging water from a fuel cell stack at fuel cell system shutdown. The method includes determining a stack water generation request to control the rate of drying of membranes in the stack and determining a cathode catalytic heating water generation request. A maximum charge a battery in the fuel cell system can accept is also determined. An ancillary power request for powering components of the fuel cell system during shutdown is determined. The method allocates how much of the water generation request will be fulfilled by operating the fuel cell stack to charge the battery and to provide the power needed for the ancillary power request, and how much of the water generation request will be fulfilled by cathode catalytic heating that produces water and heat in a cathode side of the fuel cell stack.