Species distribution models (SDMs) can be used to identify areas predicted as both suitable for rare native species and highly susceptible to invasion by alien species, at present and under future climate and land-use scenarios. To assess the condition and dynamics of such conflicts, we developed a combined predictive modelling (CPM) approach. The CPM approach predicts species distributions by combining two SDMs fitted using subsets of predictors classified as acting at either regional (e.g. climatic) or local (e.g. land-cover) scales. Combining the two predictions yielded four classes of habitat suitability of varying interest from a conservation viewpoint. We illustrate the CPM approach for an alien invader (Acacia dealbata) and a rare species (Iris boissieri) associated with similar habitats in northwest Portugal. We modelled their current and future distributions under combined scenarios of climate and land-use change. Results show that climate and land-use changes will create new conflict areas between Acacia dealbata and Iris boissieri, particularly inside the existing protected area network. The CPM approach allowed us to identify priority sites for action and contributed information to support both reactive and proactive management of invasions in conservation-relevant areas. The framework is generic and can be applied to many other systems where conflicts between alien and rare species are expected to be influenced by global change.