A fiber amplifier system comprising: an optical source providing an optical seed beam; one or more optical components that are responsive to the seed beam and each causing frequency modulation, FM, to amplitude modulation, AM, conversion that creates a non-uniform spectral transmission of the seed beam having peaks and nulls; one or more actuators (18, 42, 62) where each actuator is either positioned before a respective one of the optical components, positioned after a respective one of the optical components or coupled to a respective one of the optical components, each actuator being configured to cause a shift in the spectral transmission of the seed beam created by the respective optical component; a fiber amplifier responsive to the seed beam after the one or more actuators and the one or more optical components and configured to generate an amplified output beam; a beam sampler responsive to the amplified output beam and configured to provide a sample beam; a detector sub-system (34, 44, 46, 48, 52) responsive to the sample beam, said detector sub-system configured to detect an amount of amplitude modulation in the sample beam and configured to generate a control metric signal identifying the amount of amplitude modulation; and a spectral shift controller (36, 50) responsive to the control metric signal from the detector sub-system and configured to control the one or more actuators to cause the one or more actuators to make adjustments to cause the spectral transmission created by the one or more optical components to shift so that the peaks or nulls in the non-uniform spectral transmission align with a center frequency of the seed beam to reduce the amplitude modulation in the seed beam. an optical source providing an optical seed beam; one or more optical components that are responsive to the seed beam and each causing frequency modulation, FM, to amplitude modulation, AM, conversion that creates a non-uniform spectral transmission of the seed beam having peaks and nulls; one or more actuators (18, 42, 62) where each actuator is either positioned before a respective one of the optical components, positioned after a respective one of the optical components or coupled to a respective one of the optical components, each actuator being configured to cause a shift in the spectral transmission of the seed beam created by the respective optical component; a fiber amplifier responsive to the seed beam after the one or more actuators and the one or more optical components and configured to generate an amplified output beam; a beam sampler responsive to the amplified output beam and configured to provide a sample beam; a detector sub-system (34, 44, 46, 48, 52) responsive to the sample beam, said detector sub-system configured to detect an amount of amplitude modulation in the sample beam and configured to generate a control metric signal identifying the amount of amplitude modulation; and a spectral shift controller (36, 50) responsive to the control metric signal from the detector sub-system and configured to control the one or more actuators to cause the one or more actuators to make adjustments to cause the spectral transmission created by the one or more optical components to shift so that the peaks or nulls in the non-uniform spectral transmission align with a center frequency of the seed beam to reduce the amplitude modulation in the seed beam.