Bird migration requires high energy expenditure, and long–distance migrants accumulate fat for use as fuel during stopovers throughout their journey. Recent studies have shown that long–distance migratory birds, besides accumulating fat for use as fuel, also show adaptive phenotypic flexibility in several organs during migration. The migratory routes of many songbirds include stretches of sea and desert where fuelling is not possible. Large fuel loads increase flight costs and predation risk, therefore extensive fuelling should occur only immediately prior to crossing inhospitable zones. However, despite their crucial importance for the survival of migratory birds, both strategic refuelling decisions and variation in phenotypic flexibility during migration are not well understood. First–year thrush nightingales (Luscinia luscinia) caught in the early phase of the onset of autumn migration in southeast Sweden and exposed to a magnetic treatment simulating a migratory flight to northern Egypt increased more in fuel load than control birds. By contrast, birds trapped during the late phase of the onset of autumn migration accumulated a high fuel load irrespective of magnetic treatment. Furthermore, early birds increased less in flight–muscle size than birds trapped later in autumn. We suggest that the relative importance of endogenous and environmental factors in individual birds is affected by the time of season and by geographical area. When approaching a barrier, environmental cues may act irrespective of the endogenous time programme.