The Southern Ocean is the primary region for the uptake of anthropogenic carbon dioxide (CO2) and is, therefore, crucial for Earth’s climate. However, the Southern Ocean CO2 flux estimates reveal substantial uncertainties and lack direct validation. Using seven independent and directly measured air-sea CO2 flux datasets, we identify a 25% stronger CO2 uptake in the Southern Ocean than shipboard dataset–based flux estimates. Accounting for upper ocean temperature gradients and insufficient temporal resolution of flux products can bridge this flux gap. The gas transfer velocity parameterization is not the main reason for the flux disagreement. The profiling float data–based flux products and biogeochemistry models considerably underestimate the observed CO2 uptake, which may be due to the lack of representation of small-scale high-flux events. Our study suggests that the Southern Ocean may take up more CO2 than previously recognized, and that temperature corrections should be considered, and a higher resolution is needed in data-based bulk flux estimates.