A system for capturing carbon dioxide in flue gas includes a fuel cell assembly including at least one fuel cell including a cathode portion configured to receive, as cathode inlet gas, the flue gas generated by the flue gas generating device or a derivative thereof, and to output cathode exhaust gas and an anode portion configure to receive an anode inlet gas and to output anode exhaust gas, a fuel cell assembly voltage monitor configured to measure a voltage across the fuel cell assembly, and a controller configured to receive the measured voltage across the fuel cell assembly from the fuel cell assembly voltage monitor, determine an estimated carbon dioxide utilization of the fuel cell assembly based on the measured voltage across the fuel cell assembly, and reduce the carbon dioxide utilization of the fuel cell assembly when the determined estimated carbon dioxide utilization is above a predetermined threshold utilization.