Large-scale climatic fluctuations, such as the El Niño-Southern Oscillation, can have dramatic effects on ocean ecosystem productivity. Many mobile species breeding in temperate or higher latitudes escape the extremes of seasonal climate variation through long-distance, even trans-global migration, but how they deal with, or are affected by, such longer phased climate fluctuations is less understood. To investigate how a long-lived migratory species might respond to such periodic environmental change we collected and analysed a 13 year biologging dataset for a trans-equatorial migrant, the Manx shearwater (Puffinus puffinus). Our primary finding was that in El Niño years, non-breeding birds were at more northerly (lower) latitudes than in La Niña years, a response attributable to individual flexibility in migratory destinations. Daily time spent foraging varied in concert with this latitudinal shift, with birds foraging less in El Niño years. Secondarily, we found that in subsequent breeding, a hemisphere away, El Niño years saw a reduction in foraging time and chick provisioning rates: effects that could not be attributed to conditions at their breeding grounds in the North Atlantic. Thus, in a highly migratory animal, individuals may adjust to fluctuating non-breeding conditions but still experience cascading carry over effects on subsequent behaviour.