Beginning in the twentieth century, atmospheric deposition of N and P greatly increased in terrestrial ecosystems, including alpine grasslands. These inputs have profoundly affected soil microbial C and N cycles. Changes in the microbial environment are directly caused by changes in soil N and P availability and also indirectly through changes in vegetation in response to increased fertilization. The mechanisms involved in both the direct and indirect changes are not mutually exclusive and are poorly understood. Therefore, we investigated the responses of vegetation and soil microbes to a 9-year fertilization (N and P) experiment in an alpine grassland in the Qinghai–Tibetan Plateau in China. We found that N addition altered soil microbial community composition and processes regardless of P addition. To maintain stoichiometric homeostasis, soil microbes adjusted metabolic processes in response to changes in nutrient availability. High N availability enhanced microbial investment in C acquisition as indicated by β-1,4-Glucosidase activity. The abundance of microbial taxa that degrade labile C also increased. High N inputs also induced a proliferation of denitrifiers and increased the gaseous N loss potential. Partial least squares path modelling indicated that soil parameters (e.g., soil organic C and total N) and changes in the plant community played a key role in shaping soil microbial community structure and C and N cycling. Our results suggest that vegetation and stoichiometric differences between resource availability and soil microbial nutrient requirements collectively regulate the responses of soil microbial processes to N enrichment, which provides novel experimental insights into the mechanisms underlying the effects of nutrient inputs on microbial C and N cycles. Ultimately, our findings highlight the importance of plant traits in regulating microbial nutrient cycles, further promoting our comprehension about the mechanism of variation in the microbial nutrient cycles in an alpine grassland soils.