Transient impacts on the performance of solid oxide fuel cell/gas turbine (SOFC/GT) hybrid systems were investigated using hardware-in-the-loop simulations (HiLSs) at a test facility located at the U.S. Department of Energy, National Energy Technology Laboratory. The work focused on applications relevant to polygeneration systems, which require significant fuel flexibility. Specifically, the dynamic response of implementing a sudden change in fuel composition from syngas to methane was examined. The maximum range of possible fuel composition allowable within the constraints of carbon deposition in the SOFC and stalling/surging of the turbine compressor system was determined. It was demonstrated that the transient response was significantly impact the fuel cell dynamic performance, which mainly drives the entire transient in SOFC/GT hybrid systems. This resulted in severe limitations on the allowable methane concentrations that could be used in the final fuel composition when switching from syngas to methane. Several system performance parameters were analyzed to characterize the transient impact over the course of 2 h from the composition change.