Land clearing and ecosystem degradation are primary causes of loss of biodiversity and ecosystem services worldwide, putting at risk sustainable options for Earth and humankind. According to recent global estimates, degraded lands already account for at least 1 and up to 6 billion ha. Given high rates of habitat degradation and loss of biodiversity in human-dominated landscapes with high levels of ecosystem transformation, conventional approaches to conservation such as setting aside lands in protected areas, are not enough; in combination with ecosystem protection, ecological restoration is essential to ensure the conservation of biodiversity and delivery of ecosystem services. Despite recognition of the role of ecological restoration, the planning of restoration at the landscape scale remains a major challenge. Specifically, more studies are needed on developing restoration plans that maximize conservation and provisioning of ecosystem services, while minimizing competition with high-productivity land uses. We use Colombia, one of the world’s mega-diversity countries in which ca. 25 % of ecosystems are listed as critically endangered (CR), as a test case for exploring the potential advantages of including the Red List of Ecosystems, a newly developed tool for assessing conservation value, in restoration planning. We identified restoration priorities focused on both high-risk ecosystems and low-productivity lands, to maximize conservation value and minimize land-use conflicts. This approach allowed us to identify over 6 M ha of priority areas for restoration, targeting the restoration of 31 (75 %) of the country’s endangered ecosystems. Eight of the Regional Administrative Environmental Planning Areas (CARs) had greater than 20 % of their area identified as restoration priorities. We roughly estimated that the cost of restoring the prioritized areas with restoration through natural regeneration, using payment for ecosystem services (PES), would equal less than 50 % of the annual budget of the CARs. Our results are in sharp contrast (only 12 % agreement) with the priorities identified under the current National Restoration Strategy of Colombia, and highlight the potential contribution of the Red List of Ecosystems in refining and improving restoration planning strategies at both national and sub-national levels.