Humans are both intentionally (fertilization) and unintentionally (atmospheric nutrient deposition) adding nutrients worldwide. Increasing availability of biologically reactive nitrogen (N) is one of the major drivers of plant species loss. It remains unclear, however, whether plant diversity will be equally reduced by inputs of reactive N coming from either small and frequent N deposition events or large and infrequent N fertilization events. By independently manipulating the rate and frequency of reactive N inputs, our study teases apart these potentially contrasting effects. Plant species richness decreased more quickly at high rates and at low frequency of N addition, which suggests that previous fertilization studies have likely over-estimated the effects of N deposition on plant species loss. N-induced species loss resulted from both acidification and ammonium toxicity. Further study of small and frequent N additions will be necessary to project future rates of plant species loss under increasing aerial N deposition.