Across their ranges, different populations of migratory species often use separate routes to migrate between breeding and non‐breeding grounds. Recent changes in climate and land‐use have led to breeding range expansions in many species but it is unclear whether these populations also establish new migratory routes, non‐breeding sites and migration phenology. Thus, we compared the migration patterns of European Bee‐eaters Merops apiaster from two established western (n = 5) and eastern (n = 6) breeding populations in Europe, with those from a newly founded northern population (n = 19). We aimed to relate the breeding populations to the two known non‐breeding clusters in Africa, and to test for similarities of migration routes and timing between the old and new populations. Western Bee‐eaters used the western flyway to destinations in West Africa; the eastern birds uniformly headed south to southern African non‐breeding sites, confirming a complete separation in time and space between these long‐established populations. The recently founded northern population, however, also used a western corridor, but crossed the Mediterranean further east than the western population and overwintered mainly in a new non‐breeding area in southern Congo/northern Angola. The migration routes and the new non‐breeding range overlapped only slightly with the western, but not with the eastern, population. In contrast, migration phenology appeared to differ between the western and both the northern and the eastern populations, with tracked birds from the western population migrating 2–4 weeks earlier. The northern population thus shares some spatial traits with western Bee‐eaters, but similar phenology only with eastern population. This divergence highlights the adjustments in the timing of migration to local environmental conditions in newly founded populations, and a parallel establishment of new breeding and non‐breeding sites.