- Abstract Ammonia emissions from poultry-manure disposal and agricultural applications pose a global environmental challenge that requires the development of proper management practices. Recently, a scheme comprised of a compost-based biofilter for the treatment of high loads of ammonia emitted from poultry-manure digestion (up to 500 g NH 3 m −3 biofilter day −1 ) was suggested. In this study, we hypothesized that the high ammonia-adsorption capacity of the compost matrix creates an ammonia gradient along the biofilter that is occupied by adapted nitrifying communities, thus allowing high nitrification rates and ammonia removal. Accordingly, pilot-scale compost biofilters were constructed and batch-fed with ammonia emitted from digested poultry manure for over a year. The operation cycle included a nitrate washing step from the biofilter. Compost samples withdrawn at 20, 40 and 60 cm distance from the gas inlet were chemically characterized and analyzed for nitrification activity and nitrifier abundance and diversity. The number of ammonia-oxidizing bacteria (AOB) was 0.5–1 order of magnitude lower in the bottom section (0–20 cm), which was dominated by Nitrosomonas species, compared to the top layers which were occupied by a mixed Nitrosomonas and Nitrosospira population. In addition, ammonia-oxidizing archaea (AOA) were homogeneously distributed along the biofilter profile and their numbers were at least one order of magnitude higher than those of the AOB. Significantly lower potential nitrification activity was detected in the bottom layer, and correlated with AOB abundance. Together, the results indicate that with proper operation of compost biofilters, suitable communities of nitrifying microorganisms that are able to cope with a wide range of ammonia concentrations, sourced from manure digestion, will develop.