The main aim of this paper was to show important ecological tasks in the control systems of the small-scale biomass boilers. There is generally not much to improve in construction of the combustion chambers of the boilers,
because there has been strong development during last years towards emissions. But there is still lot to improve in the control systems. In the paper has been proposed solution of changing current relatively simple control systems by advanced continuous controller, with the aim not to increase cost of the boiler significantly. For this purpose, the experimental boiler has been equipped by additional instrumentation with extended functions, which can be later incorporated into commercially available units for the small biomass boilers, keeping all the advanced functions that have been developed. There has been shown optimized solution for grate sweeping that originally caused increased peaks in CO and hydrocarbons emissions that need to be reduced to fulfill requirements for ecological operation of the boiler. Use of the advanced control allows modification of travel distance of the grate moving mechanism and therefore sweeping the grate without causing serious disturbances in the process.