The microbial community assembly processes, stochastic versus deterministic, play a profound role in shaping ecosystem functions. However, the differences between these processes in bacterial and fungal communities, as well as in bulk and rhizosphere soils, during ecological restoration have rarely been explored. Here, we investigated the microbial community assembly during restoration of bare alpine slopes by integrating high-throughput sequencing, ecological null model, PICRUSt2, and FUNGuild analyses. Our results revealed that beta nearest taxon index (βNTI) values of the bacterial community were less than −2 in all treatments (including bare slope and ecological restoration), indicating that deterministic processes dominated bacterial community assembly. In contrast, βNTI values of the fungal community were more than −2 and less than +2 in the bare slope, while the values were less than −2 in the ecological restoration, indicating that fungal assembly shifted from stochastic drift to deterministic selection. Selection pressures on bacterial and fungal communities in the bulk soils were stronger than in the rhizosphere soils, as evidenced by the higher βNTI absolute values in the bulk soils compared to the rhizosphere. Furthermore, phylogenetic clustering intensified with restoration, driven by plant-mediated environmental filtering. The breadth of the bacterial niche correlated more strongly with the soil multifunctionality (e.g., carbon and nitrogen cycling) than with fungal niche breadth. Overall, this study reveals the community assembly of bacteria and fungi during the restoration of bare alpine slopes and emphasizes the critical role of bacterial communities in early restoration and the need for restoration strategies that account for the diverse microbial communities and their functional connections to ecosystem recovery.