Alpine meadow degradation induced by human trampling decreases plant biomass and species diversity, potentially altering soil chemistry and microbial community composition. We studied soil carbon (C), nitrogen (N) and phosphorus (P) plus soil bacterial and fungal community structure in alpine meadows, along a degradation gradient induced by human trampling at Wugong Mountain, China. As degradation increased (from 0 to 100% bare ground), pathotroph (both animal and plant hosts) and symbiotroph (especially ectomycorrhizae) fungal diversity increased but overall microbial diversity did not vary. Degradation altered fungal taxonomic composition with higher Cryptomycota and Mucoromycota diversity in more degraded sites. Path analyses indicated that fungal composition changes with degradation were mainly related to changes in soil C and P while bacterial changes were mainly related to changes in soil N and pH. Degradation modified bacterial taxonomic composition with higher Gemmatimonadetes but lower Acidobacteria, Cyanobacteria, and Planctomycetes diversity associated with lower pH, higher TN, lower NH₄⁺, and higher NO₃⁻ in more degraded areas. The results indicate that trampling impacts both soil fungal and bacterial communities but these microbial groups respond to different soil chemistry modifications. These results highlighting soil microbial community changes suggest their importance in the restoration of degraded alpine meadows with human trampling and hence the rapid recovery of their function.