A fuel cell system includes a first fuel cell having a first anode and a first cathode, wherein the first anode is configured to output a first anode exhaust gas. The system further includes a first oxidizer configured to receive the first anode exhaust gas and air from a first air supply, to react the first anode exhaust gas and the air in a preferential oxidation reaction, and to output an oxidized gas. The system further includes a second fuel cell configured to act as an electrochemical hydrogen separator. The second fuel cell includes a second anode configured to receive the oxidized gas from the first oxidizer and to output a second anode exhaust gas, and a second cathode configured to output a hydrogen stream. The system further includes a condenser configured to receive the second anode exhaust gas and to separate water and CO2.