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Abstract Mesoscale eddies are abundant in the global oceans and known to affect oceanic and atmospheric conditions. Understanding their cumulative impact on the air‐sea carbon dioxide (CO2) flux may have significant implications for the ocean carbon sink. Observations and Lagrangian tracking were used to estimate the air‐sea CO2 flux of 67 long lived (>1 year) mesoscale eddies in the South Atlantic Ocean over a 16 year period. Both anticyclonic eddies originating from the Agulhas retroflection and cyclonic eddies originating from the Benguela upwelling act as net CO2 sinks over their lifetimes. Anticyclonic eddies displayed an exponential decrease in the net CO2 sink, whereas cyclonic eddies showed a linear increase. Combined, these eddies significantly enhanced the CO2 sink into the South Atlantic Ocean by 0.08 ± 0.04%. The studied eddies constitute a fraction of global eddies, and eddy activity is increasing; therefore, explicitly resolving eddies appears critical when assessing the ocean carbon sink.