The Congolese upwelling system (CUS), located along the West African coast north of the Congo River, is one of the most productive and least studied systems in the Gulf of Guinea. The Sea Surface Temperature minimum in the CUS occurs in austral winter, when the winds are weak and not particularly favorable to coastal upwelling. Here, for the first time, we use a high-resolution regional ocean model to identify the key atmospheric and oceanic processes that control the seasonal evolution of the mixed-layer temperature in a 1°-wide coastal band from 6°S to 4°S. The model is in good agreement with observations on seasonal timescales, and in particular reproduces the signature of the surface upwelling during the austral winter, the shallow mixed-layer due to salinity stratification, and the signature of coastal wave propagation. The analysis of the mixed-layer heat budget reveals a competition between warming by air-sea fluxes, dominated by the solar flux throughout the year, and cooling by vertical mixing at the base of the mixed-layer, as other tendency terms remain weak. The seasonal cooling is induced by vertical mixing, but is not controlled by the local wind. A subsurface analysis shows that remotely-forced coastal trapped waves raise the thermocline from April to August, which strengthens the vertical temperature gradient at the base of the mixed-layer and leads to the mixing-induced seasonal cooling in the Congolese upwelling system.