The presence and interaction of shrubs and arbuscular mycorrhizal fungi (AMF) are important for the biogeochemical cycles and sustainable development of arid and semiarid ecosystems. The regulatory mechanisms of the soil microenvironment were explored by studying microbial nutrient constraints in ecosystems. Three native shrubs were planted with and without AMF inoculation in the experimental nursery of Inner Mongolia Agricultural University. The soil chemical properties; enzyme activities related to carbon (C), nitrogen (N), and phosphorus (P) acquisition; and microbial biomass C and N were measured to determine the ecoenzymatic stoichiometries and microbial nutrient limitations of the rhizosphere soils. The ratios of ecoenzymes associated with C acquisition in the rhizospheres of Spiraea pubescens were the largest, as well as microbial C limitation. In addition, Clematis fruticosa and Amygdalus mongolica inoculated with AMF significantly increased the ratios of enzymes related to C acquisition and increased microbial C limitation in the rhizospheres of these two shrubs. The ratio of N and P acquisition enzymes showed that A. mongolica and S. pubescens were significantly lower than C. fruticosa, and the lowest microbial P limitation was found in the rhizosphere soil of C. fruticosa in the noninoculated treatment; however, there was no significant difference between shrubs in the inoculated treatment. The microbial P limitation of the shrubs with AMF inoculation could be positive, negative, or not impacted. This result indicated that AMF regulated microbial P limitation in the rhizospheres of shrubs and was closely related to the accumulation of plant biomass. Partial least squares path model analysis indicated that the main influencing factors of microbial C and P limitation were glomalin-related soil protein (GRSP) and soil available nutrients (SANU). The results indicated that shrubs and AMF altered the ecoenzymatic stoichiometry of the rhizosphere soils, thus affecting soil microbial nutrient limitation through GRSP and SANU. Native shrubs with AMF inoculation can regulate soil microbial metabolism, providing a theoretical basis for vegetation restoration of degraded ecosystems in drylands.