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The subpolar Southern Ocean is a critical region where CO2 outgassing influences the global mean air-sea CO2 flux (FCO2). However, the processes controlling the outgassing remain elusive. We show, using a multi-glider dataset combining FCO2 and ocean turbulence, that the air-sea gradient of CO2 (∆pCO2) is modulated by synoptic storm-driven ocean variability (20 µatm, 1–10 days) through two processes. Ekman transport explains 60% of the variability, and entrainment drives strong episodic CO2 outgassing events of 2–4 mol m−2 yr−1. Extrapolation across the subpolar Southern Ocean using a process model shows how ocean fronts spatially modulate synoptic variability in ∆pCO2 (6 µatm2 average) and how spatial variations in stratification influence synoptic entrainment of deeper carbon into the mixed layer (3.5 mol m−2 yr−1 average). These results not only constrain aliased-driven uncertainties in FCO2 but also the effects of synoptic variability on slower seasonal or longer ocean physics-carbon dynamics. Storms dominate the subpolar Southern Ocean, where upwelling CO2 drives outgassing that impacts global CO2 budget, yet how storms modify this outgassing is unknown. Here, the authors present coupled atmosphere-ocean observations to show how storm-driven ocean mixing and circulation cause substantial CO2 variability and outgassing. [ABSTRACT FROM AUTHOR]