Abstract With the increasing demands of livestock production, grasslands are under pressure from over‐intensified grazing. Phosphorus (P) and nitrogen (N) fertilization is widely employed to meet the nutrient demands of heavy grazing. Although soil ammonia‐oxidizers play a critical role in determining N dynamics after fertilizer application, their responses to fertilization are still not well understood in steppe grassland systems. Here, the individual and combined effects of N (0, 7.5 and 15 g N m −2 year −1 ) and P (0, 3.27, 6.55 and 13.09 g P m −2 year −1 ) applications on soil ammonia‐oxidizers were explored in the Tibetan alpine steppe. Ammonia‐oxidizing archaea (AOA) and bacteria (AOB) abundance and community composition were examined using qPCR, terminal restriction fragment length polymorphism and clone libraries. Results showed that AOB diversity was significantly increased by N fertilization and decreased by P fertilization. The abundance of AOB was significantly increased by N fertilization and its interactive effects with P application. In contrast, AOA community diversity and abundance remained unaffected by either N or P application. The AOB abundance and diversity were affected by the direct effects of N fertilization, as well as its indirect effects of N application through available N and ammonium (NH 4 + ), and further analysis showed that NH 4 + and pH were the main factors. The changes to the ammonia‐oxidizing community altered the total N content of plants and the N:P ratio of Gramineae . Plant P properties were influenced by P addition, which also interacted with soil pH and available N to indirectly affect AOB. Overall, AOB exhibited stronger responses to N and P fertilization of alpine steppe grassland than AOA, and appear to play a critical role in plant nutrient absorption under fertilization management. Highlights Effects of N and P application on AOA and AOB communities were evaluated. AOB, not AOA, responded to N or P, and their interaction, and NH 4 + and pH were regulators of AOB. N application affected AOB community, resulting in changes to plant nutrient absorption. P addition affected plant tissue stoichiometry, and thus affected AOB community.