A fuel cell system includes a fuel cell stack including at least one fuel cell and a separator. Each fuel cell includes a cathode, an anode and an electrolyte between the cathode and the anode. The separator includes a membrane, and a housing defining an anode exhaust inlet, a recycled gas outlet and an exhaust gas outlet. The anode exhaust inlet and the recycled gas outlet are independently in fluid communication with the anode. The housing and the membrane defines at least in part a first chamber that is in fluid communication with the anode exhaust inlet, and a second chamber. In one embodiment, the membrane is an H2-gas permeable membrane, the recycled gas outlet is in fluid communication with the second chamber, and the exhaust gas outlet is in fluid communication with the first chamber. In another embodiment, the membrane is a CO2-gas permeable membrane, the recycled gas outlet is in fluid communication with the first chamber, and the exhaust gas outlet is in fluid communication with the second chamber.