The net flux of carbon between the Earth’s interior and exterior, which is critical for redox evolution and planetary habitability, relies heavily on the extent of carbon subduction. While the fate of carbonates during subduction has been studied, little is known about how organic carbon is transferred from the Earth’s surface to the interior, although organic carbon sequestration is related to sources of oxygen in the surface environment. Here we use high pressure–temperature experiments to determine the capacity of rhyolitic melts to carry carbon under graphite-saturated conditions in a subducting slab, and thus to constrain the subduction efficiency of organic carbon, the remnants of life, through time. We use our experimental data and a thermodynamic model of CO2 dissolution in slab melts to quantify organic carbon mobility as a function of slab parameters. We show that the subduction of graphitized organic carbon, and the graphite and diamond formed by reduction of carbonates with depth, remained efficient even in ancient, hotter subduction zones where oxidized carbon subduction probably remained limited. We suggest that immobilization of organic carbon in subduction zones and deep sequestration in the mantle facilitated the rise (~103–5 fold) and maintenance of atmospheric oxygen since the Palaeoproterozoic and is causally linked to the Great Oxidation Event. Our modelling shows that episodic recycling of organic carbon before the Great Oxidation Event may also explain occasional whiffs of atmospheric oxygen observed in the Archaean.