Carbon sequestration and biodiversity are tightly linked, but many models projecting carbon storage change do not account for the role biodiversity plays in the sequestration capacity of terrestrial ecosystems. Here, we link a macroecological model projecting changes in vascular plant richness with empirical biodiversity-biomass stock relationships, to assess the consequences of plant biodiversity loss for carbon storage under multiple climate and land-use change scenarios. Data presented here include global raster files of plant species loss by ecoregion, biomass loss by ecoregion, and carbon loss by ecoregion. Estimates are what is expected over the long term, when ecosystems approach their new equilibrium states, based on climate and land-use changes projected for 2050.This data release is associated with the publication Biodiversity loss reduces global terrestrial carbon storage published in Nature Communications.