Climate change is a major threat to biodiversity, and migratory animals are particularly vulnerable, due partly to their reliance upon good resource availability across a network of sites at specific times. Migrants perform vital ecosystem functions, transferring significant resources across large spatial scales, but the impacts of climate change on the ability of individuals to complete these journeys are poorly studied. Collecting the large-scale and long-term data on the condition of individuals during migration to address this is challenging, but in migratory birds, we have a model system for which a large network of ringers (banders) collect individual data on body size and mass, enabling variation in body condition to be tracked. We used long-term ringing data on 33 Afro–Palearctic migratory bird species at 286 sites across Europe to demonstrate a large-scale decrease in migratory fuel loads during autumn over the last 40 years, but not in spring. Declines were strongest across southern Europe and linked to rising temperatures. The timing of autumn fuelling has also shifted, occurring earlier at northern sites and later at southern sites. These relationships varied depending on diet and breeding cycle length. Obligate insectivores were more constrained by temperature in the timing and magnitude of fuelling than frugivores. Species with short breeding cycles departed later at southern sites in warmer years, likely reflecting an extended breeding season. Altogether, these latitudinally varying findings suggest a trade-off between maximising productivity or maximising adult survival as climate drives changing constraints on breeding season length and resource availability. Similar climate-induced trade-offs may be happening in other migratory taxa with the potential to influence population trends.