Creating conservation policies for declining migrant species in response to global change presents a considerable challenge. Migrant species are affected by factors at breeding grounds, overwintering areas and during migration. Accordingly, reserve-based management during the breeding season is not always a suitable conservation strategy. Recent Pied Flycatcher population decline typifies the pattern for many migrants. The UK population has declined by 43% in the past decade, but explanations, and possible solutions, remain elusive. We use 15 years of data (1990–2004) from a declining British population to establish possible reasons for decline, considering: (1) breeding performance (including the influences of competition and predation); (2) weather patterns caused by the winter phase (December–March) of the North Atlantic Oscillation (NAO), which modify conditions experienced at wintering grounds and on migration; and (3) possible impacts of climate change on spring temperatures. We conclude that decreasing breeding performance is contributing to decline, but that non-breeding factors are more important. Winter NAO index is a strong predictor of breeding population, probably because it influences food abundance in Africa and at migratory stopover points. Importantly, however, year itself enhances the predictive model, indicating that influences on population remain unaccounted for by current research. Management strategies based on increasing breeding productivity cannot fully address population decline because non-breeding factors appear important. However, as breeding performance is declining, breeding-based strategies remain useful conservation tools. To this end, our research indicates that optimal placement of nestboxes as regards orientation and habitat management to increase larval food supplies could increase productivity significantly.