Floating, organic crusts on liquid manure, stored as a result of animal production, reduce emission of ammonia (NH₃) and other volatile compounds during storage. The occurrence of NO₂^- and NO₃^- in the crusts indicate the presence of actively metabolizing NH₃ oxidizing bacteria (AOB) which may be partly responsible for this mitigation effect. Six manure tanks with organic covers (straw and natural) were surveyed to investigate the prevalence and potential activity of AOB and its dependence on the O₂ availability in the crust matrix as studied by electrochemical profiling. Oxygen penetration varied from <1 mm in young, poorly developed natural crusts and old straw crusts, to several centimeters in the old, natural crusts. AOB were ubiquitously present in all crusts investigated but nitrifying activity could only be detected in old natural crusts and young straw crust with high O₂ availability. In old natural crusts total potential NH₃ oxidation rates were similar to reported fluxes of NH₃ from slurry without surface crust. These results indicate that old, natural surface crusts may develop into a porous matrix with high O₂ availability that harbors an active population of aerobic microorganisms, including AOB. The microbial activity may thus contribute to a considerable reduction of ammonia emissions from slurry tanks with well-developed crusts.