A system and method for transitioning a firing fraction of a variable displacement internal combustion engine when generating a desired torque output. During and following the transition to the second firing fraction, a combustion recipe is ascertained and used operating the cylinders of the variable displacement internal combustion engine to generate the desired torque output. The recipe is preferably optimized for the engine operating at the second firing fraction, at least relative to the previous charge of the previous combustion recipe used with the first firing fraction.