Primary production in the global oceans fuels multiple ecosystem services including fisheries, and the open-ocean biological carbon sink, which support food security and livelihoods, and the regulation of atmospheric CO2 levels respectively. The spatial distributions of these two services are driven by primary production and it is likely that ecosystem disturbance from fishing impacts both the carbon sink and atmospheric CO2. Yet the extent of these impacts from past, present and future fishing is unknown. Here we show that 23% of global export and 40% of fishing effort are concentrated in zones of intensive overlap representing 7% of the global ocean area. This overlap is particularly evident in the Northeast Atlantic and Northwest Pacific. Small pelagic fish dominate catches in these regions and globally, and their exploitation will reduce faecal pellet carbon sinks and may cause tropic cascades affecting plankton communities important in sinking carbon. There is an urgent need to address how fisheries affect carbon cycling, and for policy objectives to include protecting the carbon sink, particularly in areas where fishing intensity and carbon export and storage are high.