Background and aims <p>While the impact of precipitation changes on plant communities has been extensively studied, its effects on desert soil and plant endophytic microbial communities remain unclear. This study conducted a simulated precipitation experiment to investigate how microbiomes in bulk soil, rhizosphere, and root endophytes of ephemeral plants respond to increased precipitation, aiming to provide new insights into microbial responses to climate change in desert ecosystems.</p> Methods <p>Three precipitation gradients were established: natural precipitation (CK), 30% increased precipitation (W1), and 50% increased precipitation (W2). High-throughput sequencing was used to analyze bacterial and fungal communities across different habitats of <i>Erodium oxyrhinchum</i>, identifying key factors driving these changes.</p> Results <p>Increased precipitation significantly boosted microbial richness, especially in the rhizosphere and endo-rhizosphere, with a more pronounced effect on fungal than bacterial. It altered bacterial community structure in bulk soil and endo-rhizosphere, and fungi in bulk soil. Furthermore, increased precipitation strengthened interspecies interactions, forming more intricate microbial networks, with bacterial networks being more intricate and more resilient to precipitation variations. Bulk soil and rhizosphere networks were larger and more stable than those in the endo-rhizosphere. These changes in microbial diversity and community structure were primarily driven by soil water content, pH, soil organic carbon, total nitrogen, and available phosphorus.</p> Conclusions <p>Increased precipitation significantly impacts the microbial communities in different habitats of desert ephemeral plants. Overall, fungal diversity was more sensitive to precipitation changes, while bacterial communities were more adaptable. Microbial networks in soil were more complex and stable than those in endophytes.</p>