A fuel cell system comprises an electrochemical fuel cell stack for generating electrical power. A load circuit is switchably coupled to the fuel cell stack for periodically receiving a discharge current from the fuel cell stack during an energy dissipation phase, such as an air stall operation for conditioning the fuel cell stack. A protection circuit is coupled to the load circuit, configured to monitor a cumulative energy dissipation level during an energy dissipation phase and to abort an energy dissipation phase if the cumulative energy level reaches a predetermined threshold. In this way, lower specification resistor components can be used for stack conditioning.