Chemical fertilizers are often used in managed grasslands to alleviate nutrient deficiency, especially for nitrogen (N) and phosphorus (P), and to maximize plant production. Soil microbial communities can respond to N/P fertilization-induced changes in soil environmental variables, like increased N availability or soil acidification, and to fertilization-induced changes in plant species richness which can determine the diversity of niches available for microbial taxa. Thus, analyzing the concurrent responses of soil environmental variables and of plant and soil microbial diversity is needed to understand the effect of N/P fertilization on soil microbial communities. Here we investigated the effects of different N, P and NP fertilization treatments (4 N levels without P; 4 P levels without N; and 4 P levels with constant N addition) on the communities of plants and of soil ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively). AOA and AOB community compositions were more sensitive to NP and N fertilization, respectively. Simple regressions and structural equation modeling demonstrate that AOA richness was correlated, though weakly, to plant species richness rather than to soil environmental variables. AOB richness was mostly correlated with plant richness and soil available P. This study demonstrates that plant richness is an important determinant of AOA and AOB richness, and helps understanding the ecology of soil ammonia oxidizers in the context of altered phosphorus and nitrogen availabilities.