A perturbation of the carbon cycle and biosphere, linked to globally increased temperatures about 55.9 million years ago, characterized the Palaeocene-Eocene Thermal Maximum. Its effect on global oceanic productivity is controversial. Here we present records of marine barite accumulation rates that show distinct peaks during this time interval, suggesting a general increase in export productivity. We propose that changes in marine ecosystems, resulting from high atmospheric partial pressure of CO2 and ocean acidification, led to enhanced carbon export from the photic zone to depth, thereby increasing the efficiency of the biological pump. Higher seawater temperatures at that time increased bacterial activity and organic matter regeneration. Through this process much of the sinking particulate organic matter was probably converted to dissolved inorganic and organic carbon. We estimate that an annual carbon export flux out of the euphotic zone and into the deep ocean waters could have amounted to about 15 Gt during the Palaeocene-Eocene Thermal Maximum. About 0.4% of this carbon is expected to have entered the refractory dissolved organic pool, where it could be sequestered from the atmosphere for tens of thousands of years. Our estimates are consistent with the amount of carbon redistribution expected for the recovery from the Palaeocene-Eocene Thermal Maximum.