To investigate the effects of shrubification—the global phenomena of an increase of shrubs in grasslands—on C, N, and P cycles, the changes in soil organic C, N, and P mineralization in an alpine meadow were compared across five plant communities: grasses and four shrub species–dominated patches. The nutrient content and stoichiometry (C:N:P) of leaves, litter, microbial biomass, and soil organic matter (SOM) were analyzed during vegetation season. Net rates of N and P mineralization were measured in situ in the top 20 cm of soil throughout the growing season, and organic C mineralization was determined under controlled conditions. Microbial C:N, C:P, and N:P ratios in the top 20 cm generally decreased with increasing plant size (height combined with crown diameter), associated with greater input of litter with lower C:nutrient ratios under shrubs. The net N and P mineralization rates in soil under shrubs were about 3- to sevenfold and 4- to 15-fold faster, respectively, compared with those under grasses. The increase in organic C mineralization under shrubs compared with that under grasses was much smaller than the increase of N or P mineralization under shrubs. This indicates faster turnover of nutrients than C leading to decoupling of organic C and nutrient mineralization across plant communities by shrubification. The C:N, C:P, and N:P ratios of organic pools mineralized in soil decreased with increasing plant size, but increased with respective microbial C:N, C:P, and N:P ratios across plant communities. This indicates that specific SOM pools were mineralized depending on plant communities and microbial stoichiometry in soil. Consequently, the decoupling of organic C and nutrient mineralization across plant communities is driven by microbial stoichiometry and increases by shrubification.