Background <p>Elucidating how plant-associated microbiome structure responds to nitrogen (N) and phosphorus (P) addition is crucial for predicting the impacts of anthropogenic disturbances on ecosystem functioning under global climate change scenarios. However, the differences in community assembly and bipartite network structure of phyllosphere and rhizosphere microbiomes under N and P addition are poorly understood. We investigated the microbiome (i.e. bacterial and fungal) communities in leaves and roots under N and P addition in a Chinese temperate meadow steppe.</p> Results <p>The results revealed that N and P addition significantly decreased the diversity and affected the community composition of bacteria and fungi in leaves and roots. The deterministic processes mainly governed the bacterial community assembly, whereas the stochastic processes primarily shaped the fungal community assembly in leaves and roots. The contribution of deterministic processes to bacterial community assembly was positively affected by N and P addition in leaves but negatively affected in roots. In contrast, the contribution of stochastic processes to fungal community assembly was negatively influenced by N and P addition in leaves but positively influenced in roots. The plant–bacterial and plant–fungal networks in both leaves and roots exhibited high specialization and modularity but low connectance and a lack of nestedness. Furthermore, N and P addition increased the complexity but decreased the stability of these networks.</p> Conclusions <p>These findings demonstrate that N and P addition affects the community assembly and network structure of phyllosphere and rhizosphere microbiomes in the grassland ecosystem.</p>