A method of controlling a gas turbine engine to provide protection against damaging pressure transients in the combustion process and to ensure compliance with emission requirements. Pressure fluctuations are monitored in a plurality of frequency ranges, and unacceptable pressure transients in different frequency ranges trigger different corrective actions. Unacceptable pressure transients in low and intermediate frequency ranges trigger a change in the pilot fuel fraction of a dual-mode combustor, while unacceptable pressure transients in a high frequency range trigger immediate power reduction in the engine. A control system for a gas turbine engine includes a plurality of timers for defining consecutive time periods for alternate monitoring of pressure transients and not monitoring pressure transients. Corrective action is taken only if unacceptable pressure transients are detected in each of the monitored time periods. As the combustion process is slowly adjusted to optimize emissions, the system will respond rapidly to an indication of an unacceptable dynamic condition.