Although migration is a widespread and taxonomically diverse behaviour, the ecological factors shaping migratory behaviour are poorly understood. Like other montane taxa, many birds migrate along elevational gradients in the tropics. Forty years ago, Alexander Skutch postulated that severe storms could drive birds to migrate downhill. Here, we articulate a novel mechanism that could link storms to mortality risks via reductions in foraging time and provide, to our knowledge, the first tests of this hypothesis in the White-ruffed Manakin (Corapipo altera), a small partially migratory frugivore breeding on the Atlantic slope of Costa Rica. As predicted, variation in rainfall was associated with plasma corticosterone levels, fat stores, plasma metabolites and haematocrit. By collecting data at high and low elevation sites simultaneously, we also found that high-elevation residents were more adversely affected by storms than low elevation migrants. These results, together with striking temporal capture patterns of altitudinal migrants relative to storms, provide, to our knowledge, the first evidence that weather-related risks incurred by species requiring high food intake rates can explain altitudinal migrations of tropical animals. These findings resolve conflicting evidence for and against food limitation being important in the evolution of this behaviour, and highlight how endogenous and exogenous processes influence life-history trade-offs made by individuals in the wild. Because seasonal storms are a defining characteristic of most tropical ecosystems and rainfall patterns will probably change in ensuing decades, these results have important implications for understanding the ecology, evolution and conservation of tropical animals.