Recent experiments exposing migratory birds to altered magnetic fields simulating geographical displacements have shown that the geomagnetic field acts as an external cue affecting migratory fuelling behaviour. This is the first study investigating fuel deposition in relation to geomagnetic cues in long-distance migrants using the western passage of the Mediterranean region. Juvenile wheatears (Oenanthe oenanthe) were exposed to a magnetically simulated autumn migration from southern Sweden to West Africa. Birds displaced parallel to the west of their natural migration route, simulating an unnatural flight over the Atlantic Ocean, increased their fuel deposition compared to birds experiencing a simulated migration along the natural route. These birds, on the other hand, showed relatively low fuel loads in agreement with earlier data on wheatears trapped during stopover. The experimental displacement to the west, corresponding to novel sites in the Atlantic Ocean, led to a simulated longer distance to the wintering area, probably explaining the observed larger fuel loads. Our data verify previous results suggesting that migratory birds use geomagnetic cues for fuelling decisions and, for the first time, show that birds, on their first migration, can use geomagnetic cues to compensate for a displacement outside their normal migratory route, by adjusting fuel deposition.