A system and method for inverting automatic frequency control applied to a reference signal used to process an input signal is disclosed. When receiving an input communication signal, a receiver controls the frequency of the reference signal to compensate for frequency differences between a transmitter and a local oscillator in the receiver. The frequency control applied to the reference signal causes frequency variations in a resultant processed signal when the input signal is processed using the reference signal. The frequency of a second reference signal is controlled such that further processing of the resultant processed signal removed effects of the frequency control applied to the reference signal. The processing which applies frequency control to the reference signal is performed in real time while the inversion process is performed in a separate processing section.