A method and apparatus for controlling engine operation to compensate for effects of combustion chamber deposits (CCDs) on combustion in a controlled auto-ignition engine is presented. Control methodologies comprise operation of variable valve actuation, fuel injection, spark timing, and intake air and coolant temperature to dynamically compensate for the effect of CCDs. A sensitivity to core gas temperature and chamber wall thermal conditions is shown, which is correlatable to in-cylinder CCD formation. Intake charge or coolant temperature control can be used to compensate for CCD effects. An engine control scheme relies upon a parametric input that quantifies instantaneous CCD formation in the combustion chamber. The result is further applicable to control pre-ignition in a conventional spark-ignition engine.