Every year, billions of songbirds migrate thousands of kilometres between their European breeding grounds and African overwintering area. As migratory birds are dependent on resources at a number of sites varying in both space and time, they are likely to be more vulnerable to environmental change. Perhaps as a consequence, long-distance migratory songbirds are declining rapidly compared to their sedentary counterparts. To understand what is driving these declines in European-Afrotropical migratory bird populations we need to understand the full annual migration cycle of these birds. Recent technological advances are currently enabling us to track yet smaller songbirds throughout their migration cycle providing valuable insight into the life cycle of individual birds. However, direct tracking of migratory birds has so far mainly been conducted on single populations and our understanding of entire species migration systems is thus still limited. In this study, we analysed the spatio-temporal migration schedule of Red-backed Shrikes, Lanius collurio, using tracking data from individuals originating from geographically distinct breeding populations (Scandinavia, the Netherlands, Spain and Greece) in the period 2009-2015. We found that populations used the same migration routes and staging sites, but segregated spatially at the main non-breeding grounds in southern Africa. This finding suggest a far more complex migration pattern than what has recently been described for European-Afrotropical migrants and provide important information for conservation management of migratory birds.