Soil enzyme activities are pivotal for diverse biochemical processes and are sensitive to land use changes. They can indicate soil microbial nutrient limitations. Nonetheless, the mechanism governing the response of soil microbial nutrient limitation to land use alterations in coastal regions remains elusive. We assessed soil nutrients, microbial biomass, and extracellular enzyme activities across various land use types—natural (wasteland and woodland) and agricultural (farmland and orchard)—in the Hangzhou Bay area, China. All four land use types experience co-limitation by carbon (C) and phosphorus (P). However, the extent of microbial resource limitations varies among them. Long-term agricultural practices diminish microbial C and P limitations in farmland and orchard soils compared to natural soils, as evidenced by lower ecoenzymatic C:N ratios and vector lengths, alongside higher microbial carbon use efficiency (CUE). Soil nutrient stoichiometric ratios and CUE are primary factors influencing microbial C and P limitations. Thus, fostering appropriate land use and management practices proves imperative to regulate soil nutrient cycles and foster the sustainable management of coastal areas.