The present invention relates to a method and system to suppress or eliminate light shift in an optical pumping system, such as an atomic clock. The method uses modulation of a radiation source, such as a radio frequency or microwave source, to simultaneously lock the frequency of the radiation source to an atomic resonance and lock the frequency of the optical pumping source in order to suppress or eliminate light shift. In one embodiment, the method of the present invention directly utilizes the out-of-phase channel of a lock-in amplifier to additionally lock an optical pumping source to a zero-light-shift frequency, where the in-phase channel is used to lock the frequency of the radiation source to an atomic resonance.