The effect of habitat choice on fuelling behaviour and the organization of migration in birds has rarely been examined, despite the potential impact of widespread anthropogenic transformation of stopover regions. High energetic requirements in migrating birds mean that resource abundance, through its influence on fuel deposition rates (FDR), is expected to be the main determinant of stopover and migration strategy. We examined the spring stopover of Tennessee Warblers (Oreothlypis peregrina) in northern Colombia, evaluating how diet, FDR, stopover duration, departure mass and estimated flight range varied between two commonly used stopover habitats: shade coffee plantations and pre-montane forests. Diet included insects in both habitats, but fruit was only consumed in pre-montane forest, where FDR was highest (FDR forest = 2.4% LBM/day; coffee = 0.5% LBM/day). Three different estimates of stopover duration suggested longer stays in coffee but lengthier durations did not result in equivalent departure mass between habitats, such that estimated flight range was twice as long for birds departing forest (2000 km) relative to coffee (1088 km). We conclude that stopover performance differed between habitats, likely influencing the subsequent temporal and spatial organization of spring migration. On the basis of flight ranges, stopovers in shade coffee may also increase the risks of trans-Caribbean flights, suggesting a mechanism by which stopover habitat could directly influence survival. Given that fruit consumption in forest probably explains these differences, we recommend the identification of appropriate fruiting trees for Neotropical agroforestry systems that can tolerate a variety of conditions and increase the quality of these anthropogenic habitats for migratory and other frugivorous birds.