A control system for an engine includes one or more processors configured to determine when a change in one or more of oxygen or fuel supplied to an engine. The one or more processors also are configured to, responsive to determining the change in oxygen and/or fuel supplied to an engine, direct one or more fuel injectors of the engine to begin injecting fuel into one or more cylinders of the engine during both a first fuel injection and a second fuel injection during each cycle of a multi-stroke engine cycle of the one or more cylinders.