A well designed and operated biomass boiler burning fuel within the specification of the boiler should not produce any smoke, but black smoke may be produced if the fuel is too wet for the boiler. All biomass boilers produce some oxides of nitrogen (NOx), particularly nitrogen dioxide (NO2).

While NOx emissions from gas boilers have been reduced significantly in recent years through the use of low NOx burners which burn at a temperature slightly below that at which NOx forms, the nature of biomass combustion, and the need to ensure the complete combustion of wood gases, means that combustion takes place at a temperature where atmospheric oxygen and nitrogen can chemically combine.

The better the quality of the combustion control system on a biomass boiler, the lower the NOx emissions will be. In general, biomass boilers produce less NOx than oil boilers. Biomass boilers do not produce any oxides of sulphur (SOx).