The intra-seasonal CO2 flux (FCO2) variability across the Southern Ocean is poorly understood due to sparse observations at the required temporal and spatial scales. Twinned Waveglider-Seaglider experiments were used to investigate how storms influence FCO2 through both the gas transfer velocity (kw) and the air-sea gradient in partial pressure of CO2 (ΔpCO2) in the sub-Antarctic zone. Winter-spring storms caused ΔpCO2 to weaken (by 15-55 μatm) due to mixing/entrainment and weaker stratification. This response in ΔpCO2 was in phase with kw resulting in a counteractive weakening in FCO2 (by 6.6 - 26.5% per storm), despite the wind-driven increase in kw. Stronger stratification during summer explained the weaker sensitivity of ΔpCO2 to storms, instead its thermal drivers dominated the ΔpCO2 variability. These results highlight the importance of observing synoptic-scale variability in ΔpCO2, the absence of which may propagate significant biases to the mean annual FCO2 estimates from large-scale observing programmes and reconstructions.