Fruit bats provide vital ecosystem services through seed dispersal aiding secondary forest regeneration. However, fruit bat species are often persecuted by fruit-growing farmers due to perceived and actual crop damage. In this study, we investigated the dietary components of Epomophorous wahlbergi, Epomophorous crypturus and Rousettus aegyptiacus, which are the three fruit bat species commonly found in litchi orchards and surrounding natural habitats in the Limpopo Province, South Africa. We further explored the contribution of fruit bats to seed dispersal and germination success. Fruit bat diet was dominated by wild fruit species (95%), while commercial fruit contributed little (2%) to their diet, even during the litchi harvest season. Fig seeds (Ficus spp.) collected from captured bats as spit outs had significantly lower germination rates than regular seeds, but a significantly lower germination latency. A similar pattern was observed for quinine trees (Rauvolfia caffra). Our results suggest that fruit bats inhabiting orchards and surrounding natural vegetation feed primarily on wild fruit trees, probably modulated by the high percentage of natural vegetation still found in our study area, supporting the importance of natural habitats in mitigating crop damage. We encourage further work on potential disservices by fruit bats and their habitat use.