Deep-sea carbonate represents Earth’s largest carbon sink and one of the least-known components of the long-term carbon cycle that is intimately linked to climate. By coupling the deep-sea carbonate sedimentation history to a global tectonic model, we quantify this component within the framework of a continuously evolving seafloor. A long-term increase in marine carbonate carbon flux since the mid-Cretaceous is dominated by a post-50 Ma doubling of carbonate accumulation to ∼310 Mt C/yr at present-day. This increase was caused largely by the immense growth in deep-sea carbonate carbon storage, post-dating the end of the Early Eocene Climate Optimum. We suggest that a combination of a retreat of epicontinental seas, underpinned by long-term deepening of the seafloor, the inception of major Himalayan river systems, and the weathering of the Deccan Traps drove enhanced delivery of Ca2+ and HCO3– into the oceans and atmospheric CO2 drawdown in the 15 m.y. prior to the onset of glaciation at ca. 35 Ma. Relatively stagnant mid-ocean ridge, rift- and subduction-related degassing during this period support our contention that continental silicate weathering, rather than a major decrease in CO2 degassing, may have triggered an increase in marine carbonate accumulation and long-term Eocene global cooling. Our results provide new constraints for global carbon cycle models, and may improve our understanding of carbonate subduction-related metamorphism, mineralization and isotopic signatures of degassing.