Abstract Life‐history traits of migratory seabirds are influenced by changing conditions at breeding and wintering grounds. Climatic conditions and predation are known to impact populations’ survival rates, but few studies examine their effect simultaneously. We used multievent capture–recapture models to assess mortality due to environmental conditions and predation in breeding European storm petrels ( Hydrobates pelagicus ) in two allopatric colonies (Mediterranean and Atlantic). Predatory mortality at the colonies showed annual variation, being around 0.05 in certain years. Mortality at sea differed between the two oceanic basins, and was lower in the Mediterranean colony [0.11, 95% CI (0.09, 0.14)] when compared to the Atlantic colony [0.18, 95% CI (0.15, 0.22)]. The Western Mediterranean Oscillation index (WeMOi) explained 57% of the temporal variability in mortality of Mediterranean breeders. In comparison, 43% of the temporal variability in mortality of Atlantic breeders was explained by the winter St Helena index (wHIX) and El Niño‐Southern Oscillation index (wENSO). Our results suggest that Mediterranean breeders remain in this basin for wintering where they may face lower migratory costs and more favourable environmental conditions. In contrast, Atlantic breeders’ mortality may be due to higher cost of migration, changing upwelling conditions in the Benguela current and heavy storms over their migratory route during La Niña events. This study underlines the importance of modelling separately different causes of mortality when testing the effects of climatic covariates.