The northern Humboldt Current system (NHCS or Peru upwelling system) sustains the world's largest small pelagic fishery. While a nearshore surface cooling has been observed off southern Peru in recent decades, there is still considerable debate on the impact of climate change on the regional ecosystem. This calls for more accurate regional climate projections of the 21st century, using adapted tools such as regional eddy-resolving coupled biophysical models. In this study three coarse-grid Earth system models (ESMs) from the Coupled Model Intercomparison Project Phase 5 (CMIP5) are selected based on their biogeochemical biases upstream of the NHCS, and simulations for the RCP8.5 climate scenario are dynamically downscaled at ∼ 12 km resolution in the NHCS. The impact of regional climate change on temperature, coastal upwelling, nutrient content, deoxygenation, and the planktonic ecosystem is documented. We find that the downscaling approach allows us to correct major physical and biogeochemical biases of the ESMs. All regional simulations display a surface warming regardless of the coastal upwelling trends. Contrasted evolutions of the NHCS oxygen minimum zone and enhanced stratification of phytoplankton are found in the coastal region. Whereas trends of downscaled physical parameters are consistent with ESM trends, downscaled biogeochemical trends differ markedly. These results suggest that more realism of the ESM circulation, nutrient, and dissolved oxygen fields is needed in the eastern equatorial Pacific to gain robustness in the projection of regional trends in the NHCS.