European rural landscapes contain high nature value farmlands that, in addition to being the main economic activity in many rural areas, host habitats and species of great conservation value. The maintenance of these farming systems largely depends on traditional ecological knowledge and the rural lifestyles of the local populations. However, they have not been sufficiently appreciated and protected, and as a result, they are currently threatened. In this study, which was performed in the Madrid region (central Spain), we analyse the social-ecological changes of the rural landscape after the establishment of a protected natural area network. The obtained results highlight a significant loss of these high nature value farming systems and a marked increase in the rewilding processes characterised by scrub–forest transition and the development of forest systems. These processes are linked to the disruption of the transmission of traditional ecological knowledge, which may imply negative consequences for both the high biocultural diversity that these systems host and the cultural identity and the socioeconomics of the rural populations that live there. A useful methodological tool is provided for social–ecological land planning and the design of effective management strategies for the conservation of rural cultural landscapes.