Eastern Boundary Upwelling Systems (EBUS) are well-known for their high productivity and fishery yields. However, being scarcely sampled and poorly represented in global models, their role as CO2 sources and sinks to the atmosphere remains elusive. Here, we present a compilation of shipboard measurements over the past two decades, showing how the Benguela Upwelling System (BUS) in the southeast Atlantic Ocean acts as a CO2 source in the north and CO2 sink in the south. Surface warming of upwelled waters increases the partial pressure of CO2 (pCO2) and outgassing in both regions, but in the south, the biologically-mediated drawdown of CO2 exceeds this warming effect. Here, the biological carbon pump owes its stronger impact on pCO2 to higher shares of upwelling source waters carrying preformed nutrients supplied from the Southern Ocean. Their formation increases pCO2 in surface waters and counteracts human-induced invasion of CO2 in the Southern Ocean. However, their utilization in the BUS compensates for over 20% of the CO2 loss occurring in the Atlantic sector of the Southern Ocean. This emphasizes the role of the BUS as key to improve our understanding of the ocean’s response to climate change and the future evolution of CO2 in the atmosphere.