A fuel cell system includes at least one topping fuel cell module including a topping anode portion configured to output a topping anode exhaust, and a topping cathode portion configured to output a topping cathode exhaust; at least one bottoming fuel cell module including a bottoming anode portion configured to output a bottoming anode exhaust, and a bottoming cathode portion configured to output a bottoming cathode exhaust; and an electrochemical hydrogen separation unit configured to receive at least a portion of the topping anode exhaust, to output a hydrogen-rich stream, and to output a CO2-rich stream. The bottoming anode portion is configured to receive the CO2-rich stream from the electrochemical hydrogen separation unit.