The Eastern Boundary Upwelling System off northwest Africa is among the most productive regions of the ocean. In 2019, two merchant ships equipped with an underway CO2 system sampled the region following exactly the same track from 10°N to 36°N. We determine the sources and sinks of CO2 and the seasonal cycle along the track. A weak permanent upwelling (WPU), a permanent upwelling (PU) and an open ocean regions are identified. The WPU (26°N to 33°N) is a source of CO2 in summer and autumn, and a sink of CO2 in winter and spring. Thermodynamic warming and cooling processes mainly drive the CO2 variations in this region. The PU (20°N to 26°N) is a sink of CO2 in spring and a source of CO2 in other seasons. This region is the most productive and exhibits the largest variability of the CO2 flux. The supply of CO2 from subsurface waters dominate over the carbon uptake by biology, which leads to a strong outgassing, especially in winter and autumn. A sink of CO2 occurs in spring only in the PU. Near Cape Blanc (20°N) in July 2019, a source of CO2 is observed around 20°N within ± 1° of latitude and becomes a sink of CO2 a few days later when the ship samples back the same area. South of 18°N, out of the influence of the coastal upwelling, the region is a sink of CO2 in winter only and the region is mainly controlled by physical processes. Using voyages from 2010 to 2022, seawater fCO2 significantly increases at a rate ranging from 1.82 μatm yr−1 to 2.10 μatm yr−1 close to the atmospheric increase. This is associated with a pH decrease between 0.0016 to 0.0022 yr−1. Nevertheless, there is no clear trend of the CO2 flux in any region.