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Abstract Background Despite our understanding of the principal factors that shape bird migration strategies, there is conflicting evidence regarding the role of habitat in shaping migration routes and schedules, including day and night activity and differences between autumn and spring. For fly-and-forage migrants, we predict that habitat characteristics might guide migration speed, route selection and migrating schedules. Methods We use solar-powered GPS transmitters, obtaining high accuracy data, to monitor the migratory movements of Eleonora’s falcon breeding in Cyprus, which is the easternmost breeding population of the species. We tested for potential preferences in habitat characteristics along the migration routes, separately for the northern, drier part and the more vegetated southern part of the trips. We also examined the relationship between migration speed and vegetative cover during day and at night, accounting for wind support. Results We found that tagged individuals repeatedly exhibited an anticlockwise loop migration pattern with spring routes being more easterly than autumn ones. We identified a preference for migration through vegetation-rich areas, where during daytime tagged individuals travel at slower migration speeds compared to vegetation-poor areas, indicating fly-and-forage activity. Birds roosted during most nights, combining refueling stopovers at selected vegetation-rich areas before or after crossing ecological barriers. Conversely, both during day and night, tagged individuals overflew unsuitable habitats more quickly. Conclusions Our results suggest that habitat is an important factor in Eleonora’s falcon migratory strategies. Active selection of vegetation rich areas in combination with reduced migration speeds there, allows the migrating falcons to combine migration during the day with fly-and-forage refueling, while roosting most nights.