Over the past three million years, Earth’s climate oscillated between warmer interglacials with reduced terrestrial ice volume and cooler glacials with expanded polar ice sheets. These climate cycles, as reflected in benthic foraminiferal oxygen isotopes, transitioned from dominantly 41-kyr to 100-kyr periodicities during the mid-Pleistocene 1,250 to 700 kyr ago (ka). Because orbital forcing did not shift at this time, the ultimate cause of this mid-Pleistocene transition remains enigmatic. Here we present foraminiferal trace element (B/Ca, Cd/Ca) and Nd isotope data that demonstrate a close linkage between Atlantic Ocean meridional overturning circulation and deep ocean carbon storage across the mid-Pleistocene transition. Specifically, between 950 and 900 ka, carbonate ion saturation decreased by 30 µmol kg−1 and phosphate concentration increased by 0.5 µmol kg−1 coincident with a 20% reduction of North Atlantic Deep Water contribution to the abyssal South Atlantic. These results demonstrate that the glacial deep Atlantic carbon inventory increased by approximately 50 Gt during the transition to 100-kyr glacial cycles. We suggest that the coincidence of our observations with evidence for increased terrestrial ice volume reflects how weaker overturning circulation and Southern Ocean biogeochemical feedbacks facilitated deep ocean carbon storage, which lowered the atmospheric partial pressure of CO2 and thereby enabled expanded terrestrial ice volume at the mid-Pleistocene transition.