Our international collaborative team in the Biodiversa funded project DarCo has published a perspective paper in npj biodiversity. Subterranean ecosystems, consisting of terrestrial, semi-aquatic, and aquatic components, face increasing threats from human activities, and existing surface-protected areas are insufficient to safeguard their biodiversity. Establishing protected areas for subterranean ecosystems is hindered by technical challenges in mapping three-dimensional systems, the rarity and endemism of subterranean organisms, and the need for collaboration among multiple stakeholders with competing interests. Despite uncertainties, our paper emphasizes the timely and critical assessment of general criteria for subterranean biodiversity protection, advocating for their implementation based on precautionary principles and proposing solutions to enhance the coverage of subterranean ecosystems within European protected areas.