Habitat maintenance as an ecosystem service (ES) is essential for the protection of natural capital, however, it is among the most challenging services for definition and evaluation. The present study is focused on assessing and mapping habitat maintenance ecosystem service in Rila and Pirin Mountains in Bulgaria for strategic planning purposes by better understanding the link between the potential of providing this ecosystem service and biodiversity in five protected areas (PAs). An integrated approach for the assessment of the condition of ecosystems in PAs and their potential to provide ecosystem services was applied and further developed in the present study. The results showed that the conservation regime allowed the territories to preserve a high degree of naturalness in a very good ecological condition – 96477 ha (73%) of the total case-study area, and 33078 ha (77%) of the target PAs, respectively. The potential of ecosystems to provide habitat maintenance ES is high to very high for 84% of the total studied area (81258.9 ha) and for 96.4% (31906 ha) of the area of the target PAs. A current assessment and mapping show the role of protected areas as spatial natural capital assets that purposefully and actively support their prioritized habitat maintenance functions as spatial guarantors for the sustenance of rich packages of material, regulating, and cultural functions in significant geographic areas. The results demonstrate the importance of protected site management in mountain areas in ensuring sustainable cooperation and consumption of ecosystem services in peripheral mountain communities of the European Union highly dependent on available natural capital.