The invention provides fuel cell systems and methods of operation where a fuel cell system is used as a backup power supply in a cold environment where the system must be maintained at a suitable temperature to allow the fuel cell to operate when needed. In one embodiment, the invention provides a thermal protection system for a fuel cell backup power generator. An enclosure houses a fuel cell and a coolant circuit. The coolant circuit is coupled to the fuel cell. A temperature sensor is provided that is adapted to indicate a system temperature. A heater is provided to increase the system temperature when actuated. For example, the heater can be an electric resistive heater or a burner coupled to a combustible fuel supply such as a propane tank. The heater can be located in the interior of the enclosure, in the coolant circuit, etc. A control circuit is provided that is adapted to actuate the heater when the system temperature is below a predetermined threshold.