In terrestrial ecosystems, resource availability and soil microbial biomass are substantially changed with ecological recovery. However, the shifts in resource stoichiometry and microbial biomass stoichiometry often do not align, leading to stoichiometric imbalance that constrains microbial growth and, consequently, affects plant community succession. The mechanisms by which soil microbes acclimate to these imbalances and how such adjustments influence plant community dynamics remain largely unexplored in alpine grasslands. To address these processes, we examined ecological stoichiometry during the secondary succession of zokor-disturbed grassland on the Qinghai–Tibet Plateau, China, utilizing a space-for-time substitution approach. Carbon (C), nitrogen (N) and phosphorus (P) contents across plant–soil–microbe and soil ecoenzymatic activities involved in soil microbial nutrient acquisition were measured. The results indicated that C:P and N:P imbalances between microbes and their plant resources intensified with the recovery of zokor-disturbed grassland. This led to phosphorus limitation in microbial growth, as indicated by the mean vector angles exceeding 45° and decreased threshold element ratio of C:P. In response, soil microbes increased their production of P-acquiring enzymes to mitigate P limitation. Through structural equation modelling (SEM), we found that the C:N:P ratios within the plant–soil–microbe systems explained 74.5% of the total variance in plant aboveground biomass. We concluded that maintaining balanced C:N:P stoichiometric ratios in plant–soil–microbe systems, facilitated by soil ecoenzymatic activities, enhances plant diversity and net primary productivity during the recovery of zokor-disturbed grassland.