The onset of migration in birds is assumed to be primarily under endogenous control in long-distance migrants. Recently, climate changes appear to have been driving a rapid change in breeding area arrival. However, little is known about the climatic factors affecting migratory birds during the migration cycle, or whether recently reported phenological changes are caused by plastic behavioural responses or evolutionary change. Here, we investigate how environmental conditions in the wintering areas as well as en route towards breeding areas affect timing of migration. Using data from 1984 to 2004 covering the entire migration period every year from observatories located in the Middle East and northern Europe, we show that passage of the Sahara Desert is delayed and correlated with improved conditions in the wintering areas. By contrast, migrants travel more rapidly through Europe, and adjust their breeding area arrival time in response to improved environmental conditions en route. Previous studies have reported opposing results from a different migration route through the Mediterranean region (Italy). We argue that the simplest explanation for different phenological patterns at different latitudes and between migratory routes appears to be phenotypic responses to spatial variability in conditions en route.