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Climate change models project shifts in precipitation patterns at regional and global scales. Increases in dry areas and the occurrence of drought predicted in future scenarios are likely to threaten grassland ecosystems. Calcareous grassland seed banks have proven to be resistant to short-term drought, but their responses to long-term drought are unknown. Here we show that 14 years of summer drought changed calcareous grassland seed bank composition, reducing its size and richness, and that these responses do not simply reflect patterns in the above-ground vegetation. Moreover, the effect of drought was larger on seed banks than on vegetation, and above-ground responses mediated by soil depth were less evident in the seed bank than in the vegetation. These results demonstrate that the severity of drought effects on calcareous grasslands is larger than previously thought, and show that this ecosystem is highly vulnerable and has low resilience to predicted decreases in soil moisture.