A system and method for selectively determining whether a freeze purge should be performed at shut-down of a fuel cell stack. The method includes identifying that the vehicle has been keyed off and then determining whether a stack membrane humidification value is less than a predetermined humidification value that identifies the humidification of membranes in fuel cells in the fuel cell stack. If the stack membrane humidification value is not less than the predetermined humidification value, then the method determines if the ambient temperature is below a predetermined ambient temperature, and if so, performs the freeze purge. If the ambient temperature is not below the predetermined ambient temperature, then the method performs a short non-freeze purge of the flow channels in the fuel cell stack. The method determines a wake-up time for a controller for a next time to determine whether a freeze purge should be performed.