A method of combustion stability control for a gas turbine engine is provided, and includes the steps of receiving by a stability controller, information regarding environmental and operating conditions, and comparing the environmental and operating conditions to pre-programmed information to determine if a likelihood of combustion instability exists. The method further includes the steps of determining optimal fuel modulation frequency and amplitude for the environmental condition to reduce combustion instability, if a likelihood of combustion instability exists, and actuating at least one fuel modulation valve to, at the optimal fuel modulation frequency and amplitude, reduce combustion instability, if a likelihood of combustion instability exists. Systems for modulating fuel flow are also provided.