ABSTRACT. Marine protected areas of multiple uses (MPA-MU), are an important management tool to protect biodiversity and regulate the use of coastal marine resources. However, robust conservation plans require an explicit consideration of not only biological but also social components, balancing the protection of biodiversity with a sustainable exploitation of marine resources. Here we applied the decision-making algorithm MARXAN to provide a zoning analysis at the Mejillones Peninsula MPA-MU in northern Chile, one of largest MPA's of the Humboldt Current Marine Ecosystem. We set conservation goals for coarse and fine-filter conservation targets that were crossed out against different threats and pressure factors from human activities across the area. We identified a portfolio of sites for conservation, within the Mejillones Peninsula MPA-MU, representing different ecological systems with different levels of human impacts and vulnerability. These results may serve as a foundational guideline for the future administration of the MPA-MU.