A fiber amplifier system including an optical component responsive to a seed beam and causing amplitude modulation that creates a non-uniform spectral transmission having peaks and nulls, and an actuator operable to shift the spectral transmission. The system further includes a fiber amplifier responsive to the seed beam and generating an amplified output beam and a beam sampler responsive to the output beam that provides a sample beam. A detector detects power fluctuations in the sample beam caused by the amplitude modulation, and generates a control metric identifying a magnitude of the fluctuations. A controller uses the control metric to control the actuator to cause it to make adjustments to the seed beam or to the optical component to cause the spectral transmission caused by the optical component to shift so that the peaks or nulls of the spectral transmission align with a center frequency of the seed beam.