A homogenous charge compression ignition engine is operated by compressing a charge mixture of air, exhaust and fuel in a combustion chamber to an autoignition condition of the fuel. The engine may facilitate a transition from a first combination of speed and load to a second combination of speed and load by changing the charge mixture and compression ratio. This may be accomplished in a consecutive engine cycle by adjusting both a fuel injector control signal and a variable valve control signal away from a nominal variable valve control signal. Thereafter in one or more subsequent engine cycles, more sluggish adjustments are made to at least one of a geometric compression ratio control signal and an exhaust gas recirculation control signal to allow the variable valve control signal to be readjusted back toward its nominal variable valve control signal setting. By readjusting the variable valve control signal back toward its nominal setting, the engine will be ready for another transition to a new combination of engine speed and load.