Glacial habitats host an astonishing diversity of species and life forms; however, most of the world’s mountain glaciers are melting due to climate change, threatening glacier biodiversity and the functioning of mountain ecosystems. In Europe, glacier retreat is particularly severe for the southernmost, peripheral chains, where the smallest glaciers occur. The European Habitat Directive includes Permanent Glaciers in the list of habitats deserving conservation, and glacial habitats host several endemic species. However, none of these species is listed in the Habitat Directive, and information on biodiversity of these environments is scarce, hindering our ability to manage mountain socio-ecological systems. PrioritIce aims at identifying trends, threats and processes acting on the biodiversity associated to glacial habitats (i.e. species living above the glacier or in glacier forelands) in Europe, with a focus on Alps and peripheral chains hosting critically endangered habitats. By combining traditional and molecular (environmental DNA) approaches, our consortium has already gathered data on 1) the distribution of key taxa (bacteria, fungi, nematodes, tardigrades, earthworms, arthropods, plants), and 2) a range of ecosystem functions (pollination, soil respiration and nutrients) from 52 study sites across the European Alps and southern European mountains. Building on these data, we will: 1) provide an exhaustive assessment of the taxonomic and functional diversity of organisms living in glacial habitats. We will complement the rich database of the consortium with additional samples from peripheral glaciers, with a special focus on poorly known endemic species; 2) analyse biological interactions to identify how species contribute to ecosystem functioning and services in glacial habitats. We will build on existing databases and develop machine learning protocols focusing on the impact of glacier extinction on the diversity–functioning relationship; 3) provide evidence-based priority programs and actions for managing glacial habitats and devising strategies for anticipating the consequences of glacier retreat under climate change scenarios. Together with a broad set of stakeholders, we will inform decision-making and environmental policy to preserve, support, and manage these ecosystems. Studying the distribution, abundance and functions of biodiversity across mountain environments, PrioritIce will enhance evidence-based protection approaches and shed light on the conservation of a poorly known, unprotected biota. Integrating statistical modelling approaches with innovative molecular methodologies will allow us to improve the ecological representation of biodiversity and its role in the functioning of glacial habitats in order to identify priority conservation areas. This will provide practitioners, managers and policy makers with the much-needed knowledge for defining adequate strategies for preserving biodiversity and mountain ecosystems.