A method of operating a fuel cell system includes providing a fuel inlet stream into a fuel cell stack, operating the fuel cell stack to generate electricity and a hydrogen containing fuel exhaust stream having a temperature above 200 C, lowering a temperature of the fuel exhaust stream to 200 C or less, separating the fuel exhaust stream into a first separated fuel exhaust stream and a second separated fuel exhaust stream, and recycling the first separated fuel exhaust stream into the fuel inlet stream.