This paper presents a systematic approach to the multivariable robust control of a hybrid fuel cell gas turbine plant. The hybrid configuration under investigation comprises a physical simulation of a 300 kW fuel cell coupled to a 120 kW auxiliary power unit single spool gas turbine. The facility provides for the testing and simulation of different fuel cell models that in turn help identify the key issues encountered in the transient operation of such systems. An empirical model of the facility consisting of a simulated fuel cell cathode volume and balance of plant components is derived via frequency response data. Through the modulation of various airflow bypass valves within the hybrid configuration, Bode plots are used to derive key input/output interactions in transfer function format. A multivariate system is then built from individual transfer functions, creating a matrix that serves as the nominal plant in an H-infinity robust control algorithm. The controller’s main objective is to track and maintain hybrid operational constraints in the fuel cell’s cathode airflow and the turbo machinery states of temperature and speed under transient disturbances. This algorithm is then tested on a SIMULINK/MATLAB platform for various perturbations of load and fuel cell heat effluence.