The Tropical Andes (TA) contain some of the most important and threatened areas for biodiversity conservation on earth. Despite the proportion of protected areas (PAs) that currently cover the TA, it is unknown if these areas are adequately protecting the biodiversity throughout the region and where the expansion of PAs is most needed to preserve biodiversity in the future. Here, we examine the conservation status of 1743 vertebrate species endemic to the TA (including mammals, birds, amphibians and reptiles), for which conservation actions should be prioritized within the region itself. Using species' geographical range maps, refined by their known elevational and habitat requirements, we carry out a gap analysis to examine to what degree endemic vertebrate species in the TA are represented by PAs. Then, using the irreplaceability-vulnerability framework, we localize first and second priority areas for conservation action, where important ecological features are subjected to severe anthropogenic disturbance. Our results show that 72% of all species and 90% of all threatened species are insufficiently covered by PAs. Furthermore, 73% of the first priority sites and 84% of the second priority sites are not covered by current PAs. These areas are predominantly located in the surroundings of major population centers in Ecuador and Colombia. To prevent species from extinction in the near future, actions to conserve their remaining habitat in prioritized areas are urgently required.