1. Protected area systems should ideally maintain adaptive and neutral evolutionary processes. To achieve this, plans for expanding protected area systems (prioritisations) can improve coverage of related attributes (evolutionary attributes). However, long-standing challenges in mapping and operationalizing evolutionary attributes have prevented their widespread usage. 2. We outline a novel framework for incorporating evolutionary processes into conservation planning. Using three amphibian species in the Iberian Peninsula (Hyla molleri, Pelobates cultripes, and Rana iberica), we mapped a comprehensive range of adaptive and neutral evolutionary attributes to delineate places containing individuals with moderate to high heterozygosity, different neutral genetic clusters, different adaptive genetic clusters, and climatic refugia. We overlaid these maps with boundaries of existing protected areas to quantify representation shortfalls and generated a prioritisation to identify additional priority areas. To assess the performance of conventional approaches, we also generated a prioritisation using only the species’ distribution data—without the evolutionary attributes. 3. We found that existing protected areas within the Iberian Peninsula are failing to adequately represent evolutionary attributes for the study species. Specifically, they are not adequately representing places predicted to contain individuals with moderate to high heterozygosity for any of the studied species, and neither are they adequately representing the species’ potential climatic refugia. They also have poor coverage of the distinct adaptive and neutral genetic clusters that comprise each of the species’ distributions. By incorporating the evolutionary attributes into the prioritization process, we identified priority areas that would address all of the shortfalls for only a minor increase in the size of the protected area system. In comparison, the prioritisation generated following conventional approaches, despite encompassing a similar extent, did not substantially improve representation of the species’ evolutionary attributes. 4. Synthesis and applications. We introduce a framework for incorporating adaptive and neutral evolutionary processes into conservation planning. This framework can reveal weaknesses in the coverage of climatic refugia, genetic diversity, and potential local adaptations by existing protected areas. Moreover, it can identify priority areas to improve conservation of evolutionary processes. Since neglecting evolutionary processes can impair conservation plans, we recommend using evolutionary data to inform decision making where possible.