Limitation of soil microorganisms by key nutrients such as nitrogen (N) and phosphorus (P) controls ecosystem processes, including soil carbon cycling. Thus, it is fundamental to estimate and understand the global patterns of microbial nutrient limitation. Using ecoenzyme stoichiometry model and 5,259 field observations of natural ecosystems in combination with Random Forest (RF) models, we predicted the global distributions of microbial N and P limitation (MNL and MPL, respectively) in global surface soils  at a resolution of 0.1 × 0.1°. The maps suggested that soil microorganisms were limited by N and P in 39 and 57%, respectively, of natural terrestrial surface areas, with 21% of areas with N and P co-limitation. As the first global assessment of spatial variation in microbial N and P limitation, our datasets could be used in Earth system models to improve projections of soil C cycling under global change.