The theory of microbial stoichiometry can predict the proportional coupling of microbial assimilation of carbon (C), nitrogen (N), and phosphorus (P). The proportional coupling is quantified by the homeostasis value (H). Covariation of H values for C, N, and P indicates that microbial C, N, and P assimilation are coupled. Here, we used a global dataset to investigate the spatiotemporal dynamics of H values of microbial C, N, and P across biomes. We found that land use and management led to the decoupling of P from C and N metabolism over time and across space. Results from structural equation modeling revealed that edaphic factors dominate the microbial homeostasis of P, while soil elemental concentrations dominate the homeostasis of C and N. This result was further confirmed using the contrasting factors on microbial P vs. microbial C and N derived from a machine-learning algorithm. Overall, our study highlights the impacts of management on shifting microbial roles in nutrient cycling.