The survival of migratory passerines depends considerably on conditions experienced on their non-breeding grounds. However, these critical non-breeding sites are generally poorly known, especially for species and populations using the eastern Afro-Palearctic flyway. To fill this gap, we measured hydrogen stable isotopes in winter-grown feathers (δ2Hf) of five long-distance migratory passerines (Eurasian Blackcap, Eastern Olivaceous Warbler, Eurasian Reed Warbler, Olive-tree Warbler, and Barred Warbler) collected during spring migration at a stopover site in Israel, a major migratory bottleneck in the Afro-Palearctic Flyway. We determined non-breeding origins of these species, for the entire migrating population and for early- and late-arriving individuals separately. We used a probabilistic model based on feather isotopes and isotopic distribution of precipitation δ2H (δ2Hp) in Africa, as well as range maps derived from species distribution models and expert opinion. While our results suggested that Reed Warbler and Olive-tree Warbler occupy most of their known range during the non-breeding season, Blackcaps migrating through Jerusalem, Israel, likely spent the non-breeding season specifically in Ethiopia and near areas, and Eastern Olivaceous Warbler concentrated in two regions in eastern tropical and central Africa. Barred Warblers’ non-breeding grounds were estimated in Kenya, but the species distribution model approach suggested additional regions. Our results further suggested that early- and late-arriving Reed Warblers spent the non-breeding season in separate areas, whereas early- and late-arriving Blackcaps migrated to the same area. Given the rapid decline in many migratory species, our results are important for a more accurate evaluation of the conditions experienced during the non-breeding season and our study is a template for refining migratory connectivity estimates for species using this important flyway.