Atmospheric CO2 concentrations declined markedly about 70,000 years ago, when the Earth’s climate descended into the last glaciation. Much of the carbon removed from the atmosphere has been suspected to have entered the deep oceans, but evidence for increased carbon storage remains elusive. Here we use the B/Ca ratios of benthic foraminifera from several sites across the Atlantic Ocean to reconstruct changes in the carbonate ion concentration and hence the carbon inventory of the deep Atlantic across this transition. We find that deep Atlantic carbonate ion concentration declined by around 25 μmol kg−1 between ~80,000 and 65,000 years ago. This drop implies that the deep Atlantic carbon inventory increased by at least 50 Gt around the same time as the amount of atmospheric carbon dropped by about 60 Gt. From a comparison with proxy records of deep circulation and climate model simulations, we infer that the carbon sequestration coincided with a shoaling of the Atlantic meridional overturning circulation. We thus conclude that changes in the Atlantic Ocean circulation may have played an important role in reductions of atmospheric CO2 concentrations during the last glaciation, by increasing the carbon storage in the deep Atlantic.