A method and system for controlling combustion in a gas turbine combustor (18) includes adjusting an amount of a premix fuel portion (30) of a pilot fuel (28) provided to a premix burner stage (48) of a pilot (46) of the gas turbine combustor. The amount of the premix fuel portion is adjusted from a preset premix fuel portion amount to an adjusted premix fuel portion amount to achieve a desired first operating condition of the combustor. An amount of a diffusion fuel portion (34) of the pilot fuel provided to a diffusion burner stage (50) of the pilot is then adjusted from a preset diffusion fuel portion amount to an adjusted diffusion fuel portion amount to achieve a desired second operating condition of the combustor.