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In this paper, a natural gas fuel processor system (FPS), a proton exchange membrane fuel cell (PEM-FC) and a catalytic burner (CB) are integrated in a combined heat power (CHP) generation plant. The FC provides the power based on electrochemical reaction of hydrogen (H2). The FPS generates the hydrogen from natural gas and the CB provides the energy for preheating the FPS inlet flows by burning any excess H2 from the FC exhaust. The coupling of these three systems poses a challenging optimization and control problem. The goal is to analyze the open loop dynamics and design a controller that achieves optimal steady state operation and acceptable transient performance, i.e., mitigates the H2 starvation and regulates reactor temperatures. We show in simulations that an observer based feedback controller, which relies on temperature measurements of two reactors, speeds up the transient response fivefold, as compared to the baseline when no feedback control is employed.