Abstract The main goal of this study is to investigate the effect of boiler design by smoke tube addition on combustion characteristics and emissions in a small scale pellet boiler. In this context, flame/smoke tube pellet-fuelled boilers with two different constructions were designed, manufactured and tested. In the design of the boilers, the first passes of gases without smoke tubes (Boiler-1) and with smoke tubes (Boiler-2) were considered. The effect of different gas passes of the boilers on flame temperature, flue gas temperature, thermal efficiency, and flue gas emissions of O2, CO, CO2 and NOx were investigated and results were compared with each other. The results showed that adding smoke tubes to the first pass of the boiler decreased the average flue gas temperatures from 87.6 °C to 76.9 °C. The thermal efficiency of the Boiler-2 geometry reached a value of 92.3% and was nearly 1.3% higher than the Boiler-1 geometry. CO emissions increased up to 205 ppm from 166 to 371 ppm by addition of smoke tubes to the first pass of the Boiler-1. It was observed that smoke tubes addition to the first pass of the boiler did not affect the NOx emissions significantly, which were about 45–47 ppm.