An integrated fuel cell stack assembly (26) and selective oxidizer bed assembly (200) is provided. The fuel cell stack assembly (26) also includes a number of fuel cells. A fuel inlet manifold (22) and fuel inlet plenum to cell stack (38) manifold are arranged in fluid communication with the fuel stack assembly (26) for supplying to and exhausting from, respectively, the fuel supply in the fuel cells in the fuel stack assembly (26). The bed resides in said fuel inlet manifold. The bed includes a selective oxidation catalyst with a heat exchange fluid conduit routed therethrough. Oxygen-containing gas is supplied into the bed via the input plenum. The temperature of the internal selective oxidizer bed is controlled by the fluid conduit in the bed to reduce carbon monoxide in the fuel.