The use of biofuels for heating purposes is beneficial from a greenhouse gas emission point of view. But combustion of solid biofuels typically is related with high emission rates of CO, NOx, PAHs, VOCs and particle matter. The most important factor that is affecting the formation of harmful emissions is the way the combustion process is organised. The amount of air injected and approach for the air supply system, are the most important factors affecting combustion process. Air staging is one of the most effective technical solutions for achieving complete combustion and low emissions. The main idea of air staging is to inject air into different zones of a combustion process. The main goal of this study is to optimise pellet combustion process in a 500 kW boiler with staged air supply. The research is based on on-site experiments and application of scientific instrumentation. Fly-away unburned fuel particles were discovered during the on-site experiments. Reduction of the amount of fly-away particles was set as a target function for the optimisation. The amount of emissions (CO, NOx and particle matter) and the amount of incombustibles in fly ashes were identified. Two different solutions with applied secondary air supply nozzles were analysed. The results of the study show that even small changes in the way the combustion air is injected can significantly affect the combustion process.