Amidst the global decline in biodiversity, there are growing calls for more ambitious conservation targets and practices, including a renewed focus on protecting and restoring natural processes. However, little is known about suitable areas for process-oriented conservation and its different strategies. In this paper, we identify priority areas for process-oriented conservation following an ecoregion-based approach. Using the Alpine Space programme area as a pilot study area, a Wilderness Quality Index is calculated and mapped based on spatial indicators reflecting variations in naturalness, human impact, remoteness, and ruggedness. To identify priority areas for process-oriented conservation, the 10% of areas with the highest wilderness quality are identified for each ecoregion (‘ecoregional approach’) and compared with the identification of the 10% wildest areas of the entire study area (‘conventional approach’). The results show significant differences in priority areas between the two approaches, with those identified by the ecoregional approach being of lower wilderness quality, more dispersed across the study region and different elevation classes, and smaller in size. The ecoregional approach results in a greater coverage of ecosystem- and species-level diversity, yet it highlights a greater need for complementing the protection of wilderness in less modified regions with rewilding initiatives and the expansion of the protected area network in ecoregions with significant human activity. Based on these findings, we discuss the potential and challenges that an ecoregion-based identification of priority areas brings for biodiversity conservation, protection and restoration practice, and local communities. The ecoregion-based approach and the findings of this study can inform initiatives under the EU Biodiversity Strategy to 2030, in particular the target to ‘strictly protect’ 10% of the EU’s land and sea.