The Humboldt coastal upwelling system in the eastern South Pacific ocean is one of the most productive marine ecosystems in the world. A weakening of the upwelling activity could lead to severe ecological impacts. As coastal upwelling in eastern boundary systems is mainly driven by wind stress, most studies so far have analysed wind patterns change through the 20th and 21st Centuries in order to understand and project the phenomenon under specific forcing scenarios. Mixed results have been reported, and analyses from General Circulation Models have suggested even contradictory trends of wind stress for the Humboldt system. In this study, we analyse the ocean upwelling directly in 13 models contributing to phase 5 of the Coupled Model Intercomparison Project (CMIP5) in both the historical simulations and an extreme climate change scenario (RCP8.5). The upwelling is represented by the upward ocean mass flux, a newly-included variable that represents the vertical water transport. Additionally, wind stress, ocean stratification, Ekman layer depth and thermocline depth were also analysed to explore their interactions with coastal upwelling throughout the period studied. The seasonal cycle of coastal upwelling differs between the Northern and Southern Humboldt areas. At lower latitudes, the upwelling season spans most of the autumn, winter and spring. However, in the Southern Humboldt area the upwelling season takes place in spring and the summertime with downwelling activity in winter. This persists throughout the Historical and RCP8.5 simulations. For both the Northern and Southern Humboldt areas an increasing wind stress is projected. However, different trends of upwelling intensity are observed away from the sea surface. Whereas wind stress will continue controlling the decadal variability of coastal upwelling on the whole ocean column analysed (surface to 300 m depth), an increasing disconnect with upwelling intensity is projected below 100 m depth throughout the 21st Century. This relates to an intensification of ocean stratification under global warming as shown by the sea water temperature profiles. Additionally, a divergence between the Ekman layer and thermocline depths is also evidenced. Given the interaction of upwelled nutrients and microscopic organisms essential for fish growth, a potential decline of coastal upwelling at depth could lead to unknown ecological and socio-economical effects.