Abstract The engine-out NOx emission from the combustion process depends on the fraction of premixed fuel burned. Hence, the study of the premixed combustion phase provides the flexibility to understand the NOx and other emissions. Here we performed an experimental study by modifying the intake charge along with pilot fueling on a twin-cylinder turbocharged CRDi diesel engine. The operating parameters, exhaust gas recirculation (EGR) and pilot injection were controlled to study about the premixed combustion phase, which gives minimum NOx emission without compromising other emissions particularly smoke. The results indicate that the premixed burn fraction decreased with an increase in pilot fuel quantity, dwell period and increased with higher EGR percentage. The optimum pilot sequences yielded a 41% reduction in NOx and 60% with smoke emissions. Also, the combination of pilot injection and EGR resulted in a drastic reduction of HC and CO emissions ∼54%.