A fuel cell system including a fuel cell stack having a plurality of fuel cells is provided. An anode supply manifold and an anode exhaust manifold are in fluid communication with the anodes of the plurality of fuel cells. A first valve is in fluid communication with the anode supply manifold and a second valve is in fluid communication with the anode exhaust manifold. A pressure sensor is adapted to measure an anode pressure. In operation, the first valve and the second valve are controlled in response to the anode pressure, thereby militating against an undesired exhausting of an anode supply stream.