The influence of chlorophyll shading on ocean dynamics has been usually disregarded in eastern boundary upwelling systems modeling studies in spite of their very high primary productivity. Here, we study how this effect impacts on the Peru upwelling system using a regional mesoscale-resolving physical biogeochemical coupled model. We show that the shading effect leads to a surface cooling of up to 1°C on the shelf due to subsurface cooling of the source waters during their transit toward the shelf. The shading effect leads to a more realistic subsurface stratification, a slowdown of the alongshore currents, and a shoaling of the oxycline. Impacts on the regional model biases show that the shading effect needs to be taken into account in both physical and coupled physical-biogeochemical regional models of upwelling systems.