Background and aims <p>Soil microbial communities are vital for ecosystem function and biodiversity, yet their composition and drivers in Mediterranean agroforestry systems remain underexplored. This study characterizes soil fungal and oomycete communities in the rhizosphere of <i>Quercus ilex</i> L. across Spanish dehesa grasslands.</p> Methods <p>High-throughput sequencing was used to assess how climate, soil properties, and tree health influence microbial alpha and beta diversity, as well as the functional traits of soil microbial communities. The study was conducted in 20 dehesas across two climatically contrasting areas of in southern Spain. In each region, five plots affected by holm oak decline and five healthy plots were selected. Soil samples were collected from six trees per plot, resulting in 120 samples.</p> Results <p>Water availability was the main driver of microbial diversity, especially for fungi. Fungal richness increased with precipitation, while oomycete alpha diversity correlated positively with clay content. Fungal communities were environmentally structured, with saprotrophic and ectomycorrhizal taxa showing distinct responses. Oomycete composition was more influenced by species interactions and their ecological roles than abiotic factors. Tree health and microbial diversity had limited effects on <i>Phytophthora cinnamomi</i> occurrence. Fungi exhibited high turnover, while oomycetes showed greater nestedness.</p> Conclusion <p>Metabarcoding reveals distinct fungal and oomycete diversity patterns in dehesas. Fungal richness and oomycete alpha diversity are shaped by water-related variables. Fungal beta diversity reflects environmental filtering, whereas oomycetes depend on biotic interactions. High fungal turnover highlights the need to preserve heterogeneity, while oomycete nestedness indicates homogenization. Fine-scale factors warrant inclusion in future management-focused research.</p> Graphical Abstract <p></p>