The control system for fuel cell gas turbine hybrid power plants plays an important role in achieving synergistic operation of subsystems, improving reliability of operation, and reducing frequency of maintenance and downtime. In this paper, we discuss development of advanced control algorithms for a system composed of an internally reforming solid oxide fuel cell coupled with an indirectly heated Brayton cycle gas turbine. In high temperature fuel cells it is critical to closely maintain fuel cell temperatures and to provide sufficient electrochemical reacting species to ensure system durability. The control objective explored here is focused on maintaining the system power output, temperature constraints, and target fuel utilization, in the presence of ambient temperature and fuel composition perturbations. The present work details the development of a centralized linear quadratic regulator (LQR) including state estimation via Kalman filtering. The controller is augmented by local turbine speed control and integral system power control. Relative gain array analysis has indicated that independent control loops of the hybrid system are coupled at time scales greater than 1 s. The objective of the paper is to quantify the performance of a centralized LQR in rejecting fuel and ambient temperature disturbances compared with a previously developed decentralized controller. Results indicate that both the LQR and decentralized controller can well maintain the system power to the disturbances. However, the LQR ensures better maintenance of the fuel cell stack voltage and temperature that can improve high temperature fuel cell system durability. © 2009 by ASME.