Neotropical fruit-eating bats play a crucial role in forest regeneration by dispersing seeds of pioneer plants from forests into deforested areas. However, later in succession bats may carry seeds in both directions. We used an isotopic approach to reveal the direction of seed transfer mediated by three co-existing short-tailed fruit bats (Carollia castanea, C. sowelli and C. perspicillata) between a forest and an adjacent mid-successional site (>15 y since deforestation); two habitats where individuals of the genus Piper differed in stable carbon isotope ratios by ~2.5‰. In a feeding experiment, we confirmed that δ13C of seeds is not altered by digestive processes. We then collected seeds defecated by bats of the genus Carollia and found that δ13C of these seeds is higher than those of Piper individuals growing in the forest, irrespective of whether bats were captured in or outside the forest. We conclude that bats of the genus Carollia were more likely to carry seeds from successional areas into the forest than in the opposite direction.