Soil water content and phosphorus availability are important factors that are expected to shape soil microbiota. Although the impacts of water deficit (drought) on soil microbiota have been reasonably studied, microbial responses to P addition combined with soil water deficit have rarely been reported, especially in relation to the identity of aboveground tree species. This study was conducted to evaluate the main and interactive effects of drought and P addition on the soil protozoa, microbial communities as determined by phospholipids fatty acids (PLFAs) and enzyme activities in a soil vegetated with N2‐fixing or non‐N‐fixing tree species and in a non‐vegetated soil. The results indicated that the effects of drought, P addition, and their interaction on soil microbiota and chemical properties varied depending on the type of aboveground tree species. Drought significantly decreased the abundance of ciliates, amoebae, total protozoa, and most of the microbial community compared to the optimum water treatment, but the effect was more pronounced under non‐N‐fixers compared to N2‐fixers. P addition significantly increased the nitrate nitrogen (NO3−‐N) and dissolve organic nitrogen (DON) in drought treated soil as compared to the well‐watered counterpart, irrespective of the planting systems. The interaction of P with drought significantly increased the mean abundance of ciliates, flagellates, amoebae, and the total protozoa in soil vegetated with non‐N‐fixers and actinomycetes PLFAs, G+ bacterial PLFAs, and total bacterial PLFAs in the soil vegetated with N2‐fixers. Our finding points to an essential role of P addition and N2‐fixing trees on soil microbiota under drought stress. This study suggests that the effects of P application depend on its interaction with drought and that drought had decreasing effects on the abundance of ciliates, flagellates, amoebae, total protozoa, and the soil microbial communities, but the extent of it effects varied with tree species.