Eastern Boundary Current Upwelling Systems are extraordinary productive regions of the World Ocean that are essential to the world’s fisheries. These upwelling ecosystems are subject to substantial variability ranging from few days to decades, and are sensitive to the expected climate change via modification of the global wind patterns. Due to their broad biological and commercial relevance, understanding the source of fluctuations and the likely climate drift of these regions is of major interest. Here we present progresses in the implementation of an end-to-end biophysical coupled model including pelagic fish in the Canary Current upwelling ecosystem. With this model approach we aim at getting new insights into how the physics, biochemistry and biology combine to give rise to the observed variability.