AbstractNiche modeling is typically used to assess the effects of anthropogenic land use and climate change on species distributions and to inform spatial conservation planning. These models focus on the suitability of local biotic and abiotic conditions for a species in environmental space (E‐space). Although movements also affect species occurrence, efforts to formally integrate geographic space (G‐space) into niche modeling have been hindered by the lack of comprehensive theoretical frameworks. We propose the “functional habitat” framework to define areas that are simultaneously of high quality in E‐space, and functionally connected to other suitable habitats in G‐space. Originating in metapopulation ecology, approaches have been developed to assess the amount of suitable connected habitats, based on the proximity between pairs of locations. Using network theory, which operates in topological space (T‐space, defined by a network), we extended these metapopulation approaches to integrate movement constraints in G‐space with niche modeling in E‐space. We demonstrate the functional habitat framework using empirical data (GPS tracking and population monitoring) throughout the European wild mountain reindeer (Rangifer t. tarandus) distribution range. We show that functional habitat outperforms traditional suitability in explaining the species' distribution. This approach integrates effects from habitat loss and fragmentation for spatial conservation planning, and avoids overemphasizing small, inaccessible areas with locally suitable habitats. The functional habitat framework formally integrates biotic, abiotic, and movement constraints in niche modeling using network theory, thus opening a wide range of applications in spatial conservation planning.