The objective of the study was to investigate a more effective use of commercially available biomass pellets (wheat straw, wood, peat) using microwave pretreatment to improve heat production. Pellets were pretreated using the originally designed microwave torrefaction device. The effects of microwave (mw) pretreatment were quantified, providing measurements of the weight loss and elemental composition of pellets and estimating the effect of mw pretreatment on their porosity, surface area and calorific values at pretreatment temperatures of T = 448–553 K. Obtained results show that the highest structural variations and elemental composition during mw pretreatment were obtained for wheat straw pellets, with an increase in reactivity, a decreasing in the duration of the thermal decomposition by about 40% and an increase in the yield of combustible volatiles. Increased reactivity of pretreated pellets enhanced the ignition and burnout of volatiles, decreasing the duration of the burnout of pretreated wheat straw, wood and peat pellets by 40%, 24% and 9%, respectively, and increasing the peak and average values of the flame temperature, heat output, and produced heat energy by 40–50%, with a correlating increase of combustion efficiency and the mass fraction of carbon-neutral CO2 emission. Thus, the applicability of microwave pretreatment for the control and improvement of heat production was confirmed.