Delayed maturity and low reproductive rate make raptors naturally sensitive to high mortality rates, yet a wide variety of human-related threats negatively affect their population dynamics and persistence over time. We modelled the variability in the proximate causes of mortality associated with six species of large migratory raptors characterized by different ecological traits. We tested the hypothesis that species-specific mortality signals occur owing to differential exposure to threats in space and time. We relied on an unprecedently large dataset of ring (band) recovery (31,269 records) over a period of >100 years. Our findings suggested that mortality of these birds has declined dramatically since the late 1970s. We found species-specific seasonal patterns of mortality, with higher mortality rates during early life-stages. For Black Kite, Common Buzzard, and Osprey, mortality increased with distance travelled and decreased with distance from migratory bottlenecks. Human-related mortality was higher than natural mortality (47% vs 5.6%), but after 1979 indirect anthropogenic factors increased, while direct ones decreased. Raptors showed differential specific exposure to mortality causes (direct human: Honey Buzzard, Marsh Harrier; indirect human: Common Buzzard, Black Kite; direct and indirect human: Osprey; natural: Montagu's Harrier). Conservation efforts and international laws have helped lower mortality caused directly by humans, but new emerging human-related threats are impacting migratory raptors and call for advanced conservation efforts. In a fast-changing world, anticipating future threats is key to stemming losses and boosting future preservation.