The present invention provides a method of treating biomass that reduces water-polluting substances, suppresses the production of malodorous gases and greenhouse gases, decreases the nitrogen content in the compost or livestock bedding thus prepared, and furthermore, easily treats nitrogen-containing biomass in a short time at high temperature. The present invention also provides compost and livestock bedding produced by the method and a biomass treating agent. The method of treating biomass includes blending, with nitrogen-containing biomass, a Geobacillus microorganism having denitrification capability and a fermentation promoter that promotes the fermentation of the nitrogen-containing biomass by the Geobacillus microorganism.