Eastern Boundary Upwelling Systems (EBUS) are highly productive ecosystems. However, being poorly sampled and represented in global models, their role as atmospheric CO2 sources and sinks remains elusive. In this work, we present a compilation of shipboard measurements over the past two decades from the Benguela Upwelling System (BUS) in the southeast Atlantic Ocean. Here, the warming effect of upwelled waters increases CO2 partial pressure (pCO2) and outgassing in the entire system, but is exceeded in the south through biologically-mediated CO2 uptake through biologically unused, so-called preformed nutrients supplied from the Southern Ocean. Vice versa, inefficient nutrient utilization leads to preformed nutrient formation, increasing pCO2 and counteracting human-induced CO2 invasion in the Southern Ocean. However, preformed nutrient utilization in the BUS compensates with ~22–75 Tg C year−1 for 20–68% of estimated natural CO2 outgassing in the Southern Ocean’s Atlantic sector (~ 110 Tg C year−1), implying the need to better resolve global change impacts on the BUS to understand the ocean’s role as future sink for anthropogenic CO2.