Human activities have increased N availability dramatically in terrestrial and aquatic ecosystems. Extensive research demonstrates that local plant species diversity generally declines in response to nutrient enrichment, yet the mechanisms for this decline remain unclear. Based on an analysis of >900 species responses from 34 N-fertilization experiments across nine terrestrial ecosystems in North America, we show that both trait-neutral and trait-based mechanisms operate simultaneously to influence diversity loss as production increases. Rare species were often lost because of soil fertilization, randomly with respect to traits. The risk of species loss due to fertilization ranged from >60% for the rarest species to 10% for the most abundant species. Perennials, species with N-fixing symbionts, and those of native origin also experienced increased risk of local extinction after fertilization, regardless of their initial abundance. Whereas abundance was consistently important across all systems, functional mechanisms were often system-dependent. As N availability continues to increase globally, management that focuses on locally susceptible functional groups and generally susceptible rare species will be essential to maintain biodiversity.