An engine control system, a controller for the engine control system, and a method of controlling a combustion process in an internal combustion engine operating at an engine operating condition. The engine control is based on closed-loop control of ignition dwell. Ignition dwell is defined as time or crank angle difference between an end of fuel injection (EOI), or some other aspect of an injection control signal, and a start of combustion (SOC), or some other aspect of an internal combustion event. One or more engine control devices, such as a fuel injector or an exhaust gas recirculation valve may be varied to control ignition dwell. By providing such a closed-loop engine control based on ignition dwell, the air/fuel charge mixture, and/or stratification present in the combustion chamber at the moment combustion starts may be controlled. Advanced combustion systems utilizing premixed compression ignition (PCI) offer the benefit of low temperature combustion for simultaneous low NOx and particulate emissions with high fuel economy. Combustion control based on ignition dwell can be used to optimize engine emissions and fuel consumption for PCI over the operating range.