A fuel cell system that employs a method for determining the potential that a freeze condition will exist after the system is shut-down based on predetermined input, such as ambient temperature, geographical location, user usage profile, date, weather reports, etc. If the system determines that a freeze condition is probable, then the system initiates a purge shut-down of the fuel cell system where water is purged out of the reactant gas flow channels. If the system determines that a freeze condition is unlikely, then it will initiate a normal shut-down procedure without purging the flow channels. The system will then periodically determine if the conditions have changed, and will initiate the purge if a freeze condition subsequently becomes probable.