Advanced combustion modes, such as PCCI, operate near the system stability limits. In PCCI, the combustion event begins without a direct combustion trigger in contrast to traditional spark-ignited gasoline engines and direct-injected diesel engines. The lack of a direct combustion trigger encourages the usage of model-based controls to provide robust control of the combustion phasing. The nonlinear relationships between the control inputs and the combustion system response often limit the effectiveness of traditional, non-model-based controllers. Accurate knowledge of the system states and inputs is helpful for implementation of an effective nonlinear controller. A nonlinear controller is developed and implemented to control the engine combustion timing during diesel PCCI operation by targeting desired values of the in-cylinder oxygen concentration, pressure, and temperature during early fuel injection.