A self-inerting fuel cell system has a membrane/electrode assembly (MEA). A first fine pore plate is positioned at an anode side of the MEA and defines a fuel reactant flow field and a coolant flow field. A second fine pore plate is positioned at a cathode side of the MEA and defines an oxidant reactant flow field and a coolant flow field. A first means drives the fuel reactant flow field; a second means drives the oxidant flow field, and a third means drives the coolant flow field at a pressure less than that of the pressures of the reactant flow fields during on load operation of the fuel cell system. An air valve is coupled to an inlet or exit port of the oxidant flow field. A controller opens the air valve and activates the reactant and coolant flow fields during fuel cell operation, and closes the air valve and de-activates the reactant and coolant flow fields during fuel cell shut down which results in coolant flooding into the reactant flow fields to thereby inert the fuel cell system during shut down.