Anthropogenic environmental changes are influencing the structure and function of many ecological communities, but their underlying mechanisms are often poorly understood. We conducted a seven-year field experiment to explore the ecological consequences of nitrogen (N) and phosphorous (P) enrichment in a high-altitude Tibetan alpine grassland. The enrichment of both N and P, but not either alone, resulted in increased plant above- and below-ground biomass. By contrast, N, but not P, enrichment reduced species richness, and altered plant phylogenetic diversity and structure. The observed decline in species richness under N addition was driven by the loss of species characterized by high leaf nitrogen content, and associated with higher soil manganese level and greater belowground competition. Our study highlights resource co-limitation of community biomass but not structure of the study grassland, while also identifying soil metal toxicity and belowground competition as important mechanisms driving community changes after nutrient amendment.