Nitrogen is essential for life and to produce food. Still, nitrogen loss of the unused nitrogen in wastewater, air, freshwater, and oceans has caused nitrogen pollution, which impacts the environment and leads to eutrophication, climate change, biodiversity loss, and ozone depletion. It also causing cardio respiratory issues in humans. Anthropogenic activities such as food processing, fertilizer production, mining, and other impacting the global biogeochemical nitrogen cycle. Autotrophic ammonia-oxidizing microbial moieties such as ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and anaerobic ammonia-oxidizing bacteria (AnAOB) are being extensively used to remove nitrogen (present in the ammonia and ammonium forms). The conventional nitrogen removal process, “nitrification and denitrification,” has been highly used in wastewater treatment plants by employing a various bacterial communities. Since it required high organic compounds and an energy-intensive process, new strategies were being developed to reduce carbon footprint. “Anammox,” “Feammox,” and “Comammox” are a few processes that utilize specific bacterial moieties and do not require organic carbon. Among these, Anammox has become the most potential nitrogen removal system. In various studies, the combined Anammox and partial nitrification (PN/A) have shown the maximum nitrogen removal rate (NRR). This review discusses the applications of autotrophic ammonia oxidizers in agriculture, wastewater treatment plants, and engineered ecosystems. We have also addressed various stress impacts on ammonia oxidizers.