Abstract Biodiversity loss is one of the great challenges of our times, and it is primarily driven by losses of natural and semi-natural areas. To avoid further biodiversity losses, landscape planning and ecosystem management could benefit from a condensed measure that tracks regional and cumulative ecological degradation from past and ongoing landscape changes. The affected species communities can be described spatially explicit by biotopes. A vulnerability map of biotopes will identify areas with a high potential to be adversely affected and a low capacity to recover. These vulnerability hot spots may require specific protection and maintenance interventions to be sustained. Following the interdisciplinary vulnerability concept, an indicator set related to landscape change was developed for the biotopes of the biosphere reserve Schorfheide-Chorin (Germany), which have been mapped as vector data according to the Brandenburg mapping key. The indicator set was structured into indicators of biotope exposure, sensitivity, and adaptive capacity. It covered patch metrics, like the size, the fractal dimension, and the amount of similar patches in the surrounding of each patch, as well as class metrics, like the mesh size, the state of endangerment and the average dispersal range of each biotope type. The resulting vulnerability index covered a biotope area of around 130,000 ha, and the study area could be extended readily. European biotopes are already mapped and monitored across large areas, primarily for nature conservation purposes. The biotope vulnerability index developed within this study is intended for application at large spatial scales and has the potential for a straightforward transfer to biotope maps from other German federal states and European regions.