Subterranean ecosystems host a broad diversity of specialized and endemic organisms that account for a unique fraction of the global taxonomic, phylogenetic, and functional diversity. Furthermore, they deliver crucial nature’s contributions to people—especially the provisioning of potable water to more than half of the world’s population. Yet, these out-of-sight ecosystems are systematically overlooked in post-2020 biodiversity and climate change targets. Only 6.9% of known subterranean ecosystems overlap with the global network of protected areas, with just a few of these areas designed to account for their vertical dimension. Two main impediments are responsible for this lack of protection. First, subterranean biodiversity patterns remain largely unmapped, even in areas with a long speleological tradition such as Europe. Second, we lack a mechanistic understanding of subterranean species' response to human-induced perturbations. The project DarCo aims to map subterranean biodiversity patterns across Europe and develop an explicit plan to incorporate subterranean ecosystems in the European Union (EU) Biodiversity Strategy for 2030. To this end, we have established a multidisciplinary team of leading scientists in subterranean biology, macroecology, and conservation science from a broad range of European countries. The project is articulated in three interconnected work packages devoted to direct research (WP2–4), plus a fourth package (WP5) aimed at maximizing the dissemination of results and engagement of stakeholders to implement practical conservation. First, by compiling existing databases and leveraging a capillary network of international collaborators, we will gather distribution data, traits, and phylogenies for all major subterranean animal groups, including crustaceans, mollusks, insects, and vertebrates (WP2). These data will serve to predict species responses to human threats using Hierarchical Modelling of Species Communities (WP3). Models' predictions of biodiversity change will provide the basis for a first dynamic mapping of subterranean life in Europe. By intersecting maps of diversity patterns, threats, and protected areas, we will design a plan to protect subterranean biodiversity complementing the current EU network of protected areas (Natura 2000), while taking into account climate-driven shifts in subterranean ecoregions (WP4). Finally, through target activities in WP5, we seek to raise societal awareness about subterranean ecosystems and invite stakeholders to incorporate subterranean biodiversity in multilateral agreements. In compliance with the European Plan S, we will make all data open and re-usable by the development of a centralized and open database on subterranean life—the Subterranean Biodiversity Platform. This will ensure that future generations will be able to build upon knowledge accumulated on subterranean biodiversity and monitor the effectiveness of today’s protection measures in the years ahead.