Amidst accelerated degradation of marine ecosystems due to anthropogenic disturbances, marine protected areas (MPAs) have been implemented globally to protect marine biodiversity, mitigate ecosystem degradation and replenish fisheries. In many countries, the creation of MPAs increased after the 2011 Aichi Targets, but in most cases, MPAs face significant operational and logistical challenges and suffer from important structural limitations that restrict their efficacy. Here, we use novel databases of taxonomic and functional diversity of 2125 coastal species (< 30 m depth), habitat continuity and climate velocities to assess the efficacy of the existing MPAs located in the Tropical, Southern, Chilean and Magellan ecoregions of the Eastern Pacific (EP). We then use optimization models to locate new MPA sites that improve protection of geographic rarity and maximize their role as climate refugia while maintaining total area protected. Existing MPAs captured between 75% and 95% of species richness in all ecoregions, largely due to the large biogeographic ranges of most species, but under-represented rare endemic species, capturing between 3% and 66%, of single-occurrence species among ecoregions. In general, MPAs are located in areas of 'moderate' to 'high' functional diversity, representing relatively well this feature within ecoregions, but less effectively across all SEP. There is a large geographical mismatch between current MPA locations and regions that might act as 'climatic refugia', which threatens the long-term conservation value of existing MPAs. Our spatial optimization models provide valuable support for enhancing the effectiveness of MPAs, through complementation or relocation, improving their efficacy to conserve different aspects of biodiversity and resilience in the face of climate change in all ecoregions. Notably, these improvements do not necessitate expanding the total area under protection, underscoring that current MPA siting did not prioritize these criteria and suggesting that modifications may be socio-politically possible.