A multi-rate audio processing system and method provides real-time measurement and processing of amplitude/phase changes in the transition band of the lowest frequency subband caused by the audio processing that can be used to apply amplitude/phase compensation to the higher subband(s). Tone signals may be injected into the transition band to provide strong tonal content for measurement and processing. The real-time measurement and compensation adapts to time-varying amplitude/phase changes regardless of the source of the change (e.g. non-linear time-varying linear or user control parameters) and provides universal applicability for any linear audio processing.