AbstractMesoscale eddies provide critical links between the atmosphere and the ocean interior modulating the exchanges of key climatic tracers across the air‐sea and mixed‐layer interface. Mesoscale eddies, widespread in the Southern Ocean, are unresolved by Earth System Models; to what extent they modify contemporary and future heat and CO₂ uptake remains unknown. The missing contribution of mesoscale eddies and their effects on properties and fluxes of heat and CO₂ are investigated in the South‐East Atlantic using a mesoscale resolving (1/12°) physical biogeochemical model. Unsupervised Self‐Organizing Maps are used to separate anticyclonic and cyclonic eddies into distinct sub‐categories based on spatial characteristics in relative vorticity. Thermal drivers dominated over non‐thermal on partial pressure of ocean CO₂ (pCO_2sw) leading to a weaker CO₂ sink in anticyclonic eddies and a stronger CO₂ sink in cyclonic eddies relative to the climatological mean. Magnitudes and depth extents of tracer anomalies scale with eddy size but are also dependent on background tracer gradients. Resolving only the largest (>50 km radii) eddies leads to underestimations in total magnitude of heat storage by 52% and 77%, and underestimations of 61% and 77% in dissolved inorganic carbon (C_T) storage for anticyclonic and cyclonic eddies respectively. The inclusion of smaller eddy features (<50 km) also offsets the asymmetry in heat and C_T storage between anticyclonic and cyclonic eddies. Resolving eddies explicitly or improvements in existing parameterizations that fail to sufficiently include eddy effects are crucial to improving estimates of heat and CO₂.