Abstract Animals select their habitat along environmental gradients, but the mechanisms that constrain the ecological requirements of an individual can differ between life stages. Dispersal is a key demographic process that determines gene flow and alters species distributions, yet few empirical studies have examined whether habitat selection in animals is changing during dispersal. In this study, we examined changes in habitat preferences during natal dispersal of red kites (Milvus milvus), a European raptor species. By deploying solar-powered GPS-GSM transmitters on nestlings, we continuously tracked individuals up to six years (2015-2020), from fledging to settlement. We applied habitat selection functions to the tracking data using hierarchical generalized additive models, a flexible method which combines individual- and population-level inference, while allowing for the contrast of the prospecting and settlement phases. During the prospecting phase (n = 204 birds), individuals were less responsive to their environment than during the settlement phase, resulting in a predicted wide distribution in Western Europe. During the settlement phase, individuals (n = 78 birds) selected a narrower range of environmental gradients, while avoiding areas of high elevation, steep topographic slopes, high human population density and highly heterogeneous landscapes. During this phase, individuals were also more philopatric, i.e., they were more inclined to choose an environment closer to their natal area, than during the prospecting phase. Suitable habitats predicted during settlement were much more spatially contrasted than during prospecting. Our study provides empirical evidence that habitat selection changes across natal dispersal phases in a long-lived species, indicating that species conservation strategies should account for different environmental constraints before and after settlement. Furthermore, our findings underscore the importance of long-term tracking data, with sufficient sample size, to study the link between habitat selection and natal dispersal.