Processes and systems for operating molten carbonate fuel cell systems are described herein. A process for operating a molten carbonate fuel cell system includes providing a hydrogen-containing stream comprising molecular hydrogen to an anode portion of a molten carbonate fuel cell; controlling a flow rate of the hydrogen-containing stream to the anode such that molecular hydrogen utilization in the anode is less than 50%; mixing anode exhaust comprising molecular hydrogen from the molten carbonate fuel cell with a hydrocarbon stream comprising hydrocarbons, contacting at least a portion of the mixture of anode exhaust and the hydrocarbon stream with a catalyst to produce a steam reforming feed; separating at least a portion of molecular hydrogen from the steam reforming feed; and providing at least a portion of the separated molecular hydrogen to the molten carbonate fuel cell anode.