All organisms need elements in fixed proportions for carrying out normal metabolic processes and how flexible they are depends on how effective they are utilizing these resources from external sources. It is important to understand the interactions among plant, soil and microbial biomass carbon (C), nitrogen (N) and phosphorus (P) stoichiometry under different conditions of resource supply. We conducted a pot experiment on 1-year-old Robinia pseudoacacia seedlings for nearly 5 months under different water, nitrogen and phosphorus supplies, and we determined plant, soil and microbial biomass C, N and P stoichiometry. We found that plant, soil and microbial nutrients and stoichiometry exhibited a certain degree of plasticity in response to the changes in water and nutrient conditions in their environments. Variation partitioning analysis showed that root stoichiometry accounted for a large part of the variance in microbial stoichiometry. Structural equation modeling further revealed that root stoichiometry and leaf stoichiometry were two direct factors affecting microbial biomass C:N and C:P, and that root stoichiometry had the greatest direct effect. In addition, the degree of homeostasis for microbial biomass C and C:P was more sensitive to changes in soil nutrients than changes in other factors, and other elements and elemental ratios displayed strict homeostasis. These results highlight the importance of studying microbial stoichiometry in improving our understanding of nutrient cycling of the plant–soil system under different water and nutrient supply.