Climate change is likely to alter the relative abundances of plant functional groups and the interactions between plants and soil microbes that maintain alpine meadow ecosystems. However, little is known about how warming-induced alterations to aboveground biomass (AGB) affect soil nutrients and microbial communities. We investigated plant community characteristics in 2002–2009 and analyzed soil properties and the soil microbial community in 2007–2009 to study the effects of warming in Qinghai Province, China. Sampling involved the use of warmed open top chambers, the monitoring of plant community characteristics, the quantification of total and available amounts of soil nutrients, and the evaluation of microbial community composition using phospholipid fatty acid (PLFA) analysis. Experimental warming initially significantly increased the number of plant functional groups and plant community AGB; however, plant community diversity and species richness decreased. Nevertheless, all these variables stabilized over time. Fungal and bacterial abundance, total nitrogen, available nitrogen and soil organic matter increased with warming, while microbial PLFAs decreased. These findings demonstrated that climate change drivers and their interactions may cause changes in soil nutrients and the abundance and content of soil microbial PLFAs. Elevated temperature has strong effects on aboveground grass biomass. Surface conditions and disturbance affect the soil microbial communities of deep soil layers.