In the Anthropocene, the pervasive impacts of climate change on arid ecosystems are increasingly evident, resulting in significant alterations in both biodiversity and functionality. Although soil microbes are anticipated to be sensitive to changes in precipitation regimes, the mechanisms through which multifaceted precipitation changes impair the delivery of multiple functions by multitrophic microbiota in soils remain largely unexplored. In the drylands of Northwestern China, we examined the direct effects of historical precipitation regimes on the soil multifunctionality of biocrusts, a model system, and their indirect impacts mediated by microbial communities. Among abiotic predictors, precipitation variability, rather than mean annual precipitation, emerged as the primary driver of multifunctionality, leading to a convergence of less functionally beneficial species. By utilizing a biodiversity-ecosystem function relationship framework, our results underscore the crucial roles ofα- andβ-diversity of heterotrophic bacteria, fungi, and phototrophic cyanobacteria in maintaining soil functionality. However, the underlying mechanisms are distinct. We found that the local richness of heterotrophs and phylogenetic dissimilarity of photoautotrophs exert positive influences on multifunctionality, while species replacement, a component ofβ-diversity, primarily enhances the variance in soil multifunctionality. Importantly, the findings illuminate the cascading effect of precipitation variability on dryland ecosystems, amplified by microbial diversity, potentially triggering a silent collapse of vulnerable arid habitats. Our study highlights the importance of considering indirect climate impacts via soil microbiota, contributing to a deeper understanding of the real-world consequences of climate change on drylands, and offering valuable insights for the management of biodiversity theory-inspired ecosystem restoration.