Land-use change influences biodiversity in non-random ways, affecting some species and functional groups more than others, with potential implications for the loss or degradation of important ecological processes, such as seed dispersal. Here we investigate the effect of patch-size reduction on the composition and functional richness (FRic) of avian communities in Atlantic Forest fragments, focusing on morphological traits associated with seed dispersal in frugivorous birds. We found that FRic of three key traits—hand-wing index, body mass and gape width—decreased with patch size reduction, because species with larger values for morphological traits were lost through local extinction. The relative absence of large-gaped and more-dispersive frugivores in small forest fragments has important implications because these species play a pivotal role in seed dispersal, carrying higher seed loads for longer distances, and consuming larger-sized seeds that cannot be dispersed by smaller-gaped frugivores. Our results highlight the importance of preserving large or interconnected habitat patches, and promoting habitat restoration of cleared areas, to ensure that sufficient avian functional diversity is maintained to supply the full range of seed dispersal services required by tropical forests, both currently and in future.