This paper studies a novel control methodology aimed at regulating and tracking turbo machinery synchronous speed and fuel cell mass flow rate of a SOFC/GT hardware simulation facility with the sole use of airflow bypass valves. The hybrid facility under consideration consists of a 120 kW auxiliary power unit gas turbine coupled to a 300 kW SOFC hardware simulator. The hybrid simulator allows testing of a wide variety of fuel cell models under a hardware-in-the-loop configuration. Small changes in fuel cell cathode airflow have shown to have a large impact on system performance. Without simultaneous control of turbine speed via load or auxiliary fuel, fuel cell airflow tracking requires an alternate actuator methodology. The use of bypass valves to control mass flow rate and decouple turbine speed allows for a greater flexibility and feasibility of implementation at the larger scale, where synchronous speeds are required. This work utilizes empirically derived transfer functions (TF) as the system model and applies a fuzzy logic (FL) control algorithm that can be easily incorporated to nonlinear models of direct fired recuperated hybrid plants having similar configurations. This methodology is tested on a SIMULINK/matlab platform for various perturbations of turbine load and fuel cell heat exhaust.