A high efficiency fuel cell system includes a topping fuel cell assembly that includes a topping cathode portion and a topping anode portion, as well as a bottoming fuel cell assembly that includes a bottoming cathode portion and a bottoming anode portion. The assembly also includes a flue gas generating device configured to provide flue gas to the topping cathode portion and/or the bottoming cathode portion, and an oxidizer assembly configured to (i) oxidize anode exhaust output from the bottoming anode portion with air and/or oxygen to generate carbon dioxide-containing exhaust and (ii) generate waste heat for heating the flue gas before the flue gas is provided to the topping cathode portion and/or the bottoming cathode portion. A separation assembly is configured to receive the carbon dioxide-containing exhaust from the oxidizer assembly and to separate carbon dioxide from the carbon dioxide-containing exhaust.