Biogas production transforms organic matter into methane, carbon dioxide and ammonia (NH3). The aim of this study was reducing NH3 emissions from liquid effluents of agricultural anaerobic digesters. An alternative to classic nitrification-denitrification was tested: partial nitrification of the ammonium-rich effluent and its recycling into the digester for nitrite conversion into dinitrogen gas (N2) via denitrification or anaerobic ammonium oxidation (Anammox). Two laboratory-scale bioreactors were set-up to this effect. In the first reactor, short residence time and oxygen-limited conditions were guaranteed. The second was filled with digested manure simulating the final stage of a plug-flow anaerobic digester. The feed was artificially amended with nitrtite (NO2-), simulating the effluent of the first reactor. Ammonium (NH4+) removal efficiencies higher than 80% were reached in the aerobic reactor, producing a NO2--rich effluent. However, mass balance showed a large percentage of “nitrogen losses”. This can either be explained by denitrification or Anammox occurring in anoxic zones inside the reactor or by aerobic denitrification, an interesting but not yet fully understood process. The anaerobic reactor removed about 90% of nitrite fed and during a certain period also approximately 80% of ammonium was degraded. Using FISH analysis, Anammox bacteria were identified in the microbial community of this reactor.