Mesoscale eddies are known to influence the Southern Ocean biogeochemistry. However, the distinct contributions of cyclonic and anticyclonic eddies to air-sea CO₂ fluxes, as well as their longer-term effects remain poorly studied. We present results from a 27-year global eddy-resolving ocean-biogeochemical simulation. We used the Okubo-Weiss parameter to classify the modeled flow regimes into cyclonic and anticyclonic eddies, peripheries, and the surrounding background waters. Our results reveal a heterogeneous influence of eddies depending on the region, driven by regional differences in eddy intensity and the gradients in background properties. The factors controlling CO₂ fluxes within eddies follow the same degree of importance as in background waters, with ∆pCO₂ being the dominant factor. This is driven primarily by changes in dissolved inorganic carbon. Our analysis shows that eddies act as a persistent carbon sink on decadal timescales, while their influence on shorter timescales is more variable and strongly shaped by eddy polarity. Anticyclonic and cyclonic eddies and periphery account for around 10 % of the Southern Ocean’s carbon uptake, with anticyclonic eddies showing the highest carbon uptake per unit area. The ability of eddies to absorb carbon computed in our results is consistent with recent observational estimates, confirming that the model realistically represents the influence of mesoscale eddies on CO₂ fluxes. Above all, our results underscore the role of mesoscale eddies in enhancing carbon uptake across the Southern Ocean.