This paper is based on the analysis of the solar combisystem installed in a 4-storey apartment building in Sigulda, Latvia. The combisystem consists of: 42 m2 of flat plate solar collectors, a 2.35 m3 accumulation tank and a 100 kW pellet boiler as the auxiliary heater. This paper focuses on the optimisation of the thermal performance of the pellet boiler. During laboratory tests on the 25 kW pellet boiler, the influence of the supply ratio of the combustion air, the chemical and heat losses in the flue gases on the performance of the boiler was stablished. The results demonstrate the optimum thermal performance, CO emissions, chemical and heat losses, which are related to the amount of free oxygen (O2) in the flue gases. The results of the laboratory tests were then applied to optimise the operation of the 100 kW pellet boiler. The flue gas measurements for the 100 kW boiler were performed in order to identify the O2 concentration, CO emissions and flue gas temperature. The results showed that what is required to optimise performance is to reduce the amount of air supplied to the boiler’s combustion chamber. Changes were made to the boiler’s control algorithms to achieve the desired result. Additionally, boiler performance was improved by changing the location of the air intake point. Decreasing temperatures in the heat accumulation tank were achieved by making modifications to the boiler’s control algorithms.