Treating NH₃-loaded gases is necessary for improved livestock management. Nitrification, the sequential oxidation of NH₃ to NO₃^—- via NO₂^—, is an important microbial process for effective long-term NH₃ removal. Denitrification, a microbial respiration process that reduces NO₃^—- and NO₂^— to N₂ under anaerobic conditions, can also contribute to nitrogen conversion in biofiltration systems. Understanding these microbial processes is imperative to control NH₃ removal better and achieve nitrogen balance in biofiltration. In this review, we discuss the functions and compositions of the microbial community responsible for nitrification and denitrification in a biofiltration system, along with the relationship between these processes and the nitrogen mass balance. Our results indicate that both nitrification and denitrification could be achieved by a consortium of microbes well adapted to the ecosystem in a full- scale biofilter. Moreover, the microbial community was controlled by substrate availability. Nitrogen removal potential was up to 39% in a laboratory-scale biofilter with intermittent water recirculation, and the unknown nitrogen loss was considered mainly denitrified. Under gradual accumulation of nitrogenous compounds, the gamma proteobacterial group contributes to NH₃ oxidization. These findings will improve our understanding of microbial fluctuations and the complex behavior of nitrifiers and denitrifiers within an NH₃-loaded biofiltration system.