A method of operating a PEM fuel cell including an anode feed circuit and a cathode feed circuit for feeding of an anode side with a reactant gas and for feeding a cathode side with a cathode gas. A shut-down mode for shutting down an electricity generating operation of the fuel system includes decreasing the supply of reactant gas and cathode gas in response of a shut-down signal, monitoring an output voltage of at least one cell of a fuel cell stack, monitoring the reactant gas pressure and the cathode gas pressure, electrically shunting of the at least one fuel cell in response of the output voltage reaching a predefined voltage level, at least reducing the pressure of the anode side to a predefined pressure level by means of at least one pump, and filling and/or flushing of at least the anode side with an inert gas.