Nitrogen (N) pollution is a global threat to the biodiversity of many plant communities, but its impacts on grassland soil seed banks are unknown. Here we show that size and richness of an acid grassland seed bank is strongly reduced after 13 years of simulated N deposition. Soils receiving 140 kg N ha(-1) per year show a decline in total seed abundance, seed species richness, and the abundance of forbs, sedges and grasses. These results reveal larger effects of N pollution on seed banks than on aboveground vegetation as cover and flowering is not significantly altered for most species. Further, the seed bank shows no recovery 4 years after the cessation of N deposition. These results provide insights into the severe negative effects of N pollution on plant communities that threaten the stability of populations, community persistence and the potential for ecosystems to recover following anthropogenic disturbance or climate change.