A method and system for controlling combustion in a gas turbine engine (10) includes reducing an overall fuel flow provided to a stage (22) of burners (e.g. 34, 35) of the gas turbine engine until reaching a predetermined dynamic operating condition of the first burner of the stage. The method also includes maintaining, while continuing to reduce the overall fuel flow (e.g. 30), a first portion (e.g. 36), of the overall fuel flow delivered to the first burner at a maintenance level so that the predetermined dynamic operating condition of the first burner is maintained.