A gas turbine engine includes a fuel cell assembly including a fuel cell stack and defining a fuel cell assembly operating parameter, a fuel source, and a turbomachine. The turbomachine includes a compressor section, a combustor, and a turbine section arranged in serial flow order. The combustor is configured to receive a flow of fuel from the fuel source and further configured to receive output products from the fuel cell stack. A controller is configured to perform operations including receiving data indicative of system operation conditions, determining a set of fuel cell operating conditions to move the system emission output into or maintain the system emission output within an emissions range, and controlling the fuel cell assembly operating parameter according to the determined set of fuel cell operating conditions.