A multi-stack fuel cell system includes upper and lower housings defining interior chambers in corresponding upper and lower stacks of fuel cells are disposed. A heat exchanger assembly is fluidly coupled with the interior chambers. The heat exchanger assembly receives input fuel and/or input air from outside of the housings and receives outgoing fuel and/or outgoing air from the fuel cells. The heat exchanger assembly heats the input fuel and/or the input air, and/or cools the outgoing fuel and/or the outgoing air. The heat exchanger assembly may be disposed between the upper and lower housings. The upper housing an upper stack of fuel cells and/or the heat exchanger assembly may assist in compressing the fuel cells in the lower stack against each other.