A large volume between compressor and turbine is present in fuel cell gas turbine hybrid systems. The substantially larger compressor plenum volume modifies the dynamic behaviour of these systems, increasing the risk of compressor surge during transients and subsequent destruction of both turbomachinery and fuel cell components. Diverting part of the compressor inlet flow directly to the turbine inlet through a cold-air bypass valve, bypassing the fuel cell stack, has been proven to be an effective method to increase the surge margin during normal operation and also to recover the machine from fully developed surge. This study investigates the dynamic effect of different cold-air bypass valve opening/closing procedures, especially steps and ramps changing the valve fractional opening. This analysis was carried out with reference to the Hybrid Performance (Hyper) facility: a hybrid system emulated using hardware and a cyber-physical fuel cell system at the National Energy Technology Laboratory (NETL), U.S. Department of Energy (DOE). Simulations performed on a Matlab®-Simulink® dynamic model of the system based on Greitzer’s theory showed a different behaviour varying the valve fractional opening with steps or ramps. Many experimental tests were performed on the Hyper facility to confirm the trends obtained from the simulations results. From the outcomes of this study, it has been possible to determine how to maximize the surge recovery effect of the cold-air bypass valve opening and to minimize surge related risks during the valve closure.