Land-use change is a major driver of the global biodiversity crisis, mainly via the fragmentation and loss of natural habitat. Although land-use changes will accelerate to meet humankind’s growing demand for agricultural products, conservation planning rarely considers future land uses and how they may affect the connectivity of ecological networks. Here, we integrate land-use models with landscape fragmentation and connectivity analyses, to assess the effects of past and future land-use changes on the connectivity of protected area networks for a highly dynamic region in southeast Spain. Our results show a continued geographical polarisation of land use, with agricultural intensification and urban development in the coastal areas, and the abandonment of traditional land use in the mountains (e.g., 1100 km2 of natural vegetation are projected to be lost in coastal areas whereas 32 km2 of natural vegetation would recover in interior areas from 1991 to 2015). As a result, coastal protected areas will experience increasing isolation. The connectivity analyses reveal that the two protected area networks in place in the study area, the European “Natura 2000” and the Andalusian “RENPA” networks, include many landscape connectors. However, we identify two areas that currently lack protection but contain several important patches for maintaining the region’s habitat connectivity: the northwestern and the southwestern slopes of the Sierra Cabrera and Bédar protected area. Our results highlight the importance of considering future land-use trajectories in conservation planning to maintain connectivity at the regional scale, and to improve the resilience of conservation networks.