Soil microbial communities play a key role in the functioning of terrestrial ecosystems, in particular through their interaction with above-ground plants and weathering of rocks. In this study, the chemical properties and microbial diversity of soils covered by different organisms on Leshan Giant Buddha body were analyzed. The results showed that the concentration of soil total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) increased significantly with the change of above-ground organisms from lichens to bryophytes and vascular plants. TOC, TN, TP, C:N, and C:P were significantly correlated with the composition of microbial community. Bacterial and fungal diversity responded differently to the change of organisms, and the diversity of bacterial communities changed significantly among different sites. The settlement of Embryogenic plants increased the α-diversity indices including Sobs, Shannon, Ace and Chao indices, which were highest in sites covered with Ferns. The relative abundances of Chloroflexi, Acidobacteria, Nitrospirae and Planctomycetes increased with the order of Bryophyte, Fern, Grass and Shrub, and Cyanobacteria was opposite, with the highest in samples covered with lichens. These results improve understanding of plant–fungi–bacteria interactions during the early stages of soil development, and provide a scientific basis for protection of Leshan Giant Buddha.