Habitat fragmentation is causing the collapse of seed dispersal interactions and ecosystem functioning. When management and conservation strategies aim to sustain ecosystem functioning of fragmented forests, species’ traits and functional performance are critical in guiding decisions. However, to date, we lack a quantitative understanding of the role of frugivores’ body size and dispersal ability in ecosystem sustainability among fragmented forests. Focusing on avian frugivory and seed dispersal in a multi-island setting, we address the data gap by recording more than 20,000 frugivory events in an artificial insular fragmented landscape constructed in 1959 and nearby unfragmented forests on the mainland. We show that large-bodied and dispersal-limited frugivorous birds are largely confined to large islands and the unfragmented mainland, whereas on small islands, small-bodied and highly mobile birds predominantly engage in frugivory interactions. The plant–frugivore meta-network exhibits a distinct compartmentalization, driven by island area and bird mobility. Birds with smaller size and greater mobility have higher topological importance, and the presence of small-bodied birds significantly enhances meta-network robustness. These results suggest that among insular fragmented forests where frugivory interactions are degraded, small-bodied and highly mobile birds disproportionately contribute to meta-community cohesion and ecosystem functioning because of the lack of large-bodied and dispersal-limited birds. We thus advocate for the restoration of landscapes to facilitate seed dispersal and functional connectivity, ensuring the presence of large patches along with small patches as stepping-stones. Meanwhile, we recommend prioritizing conservation on small-bodied and highly mobile birds in fragmented landscapes, a subset of underappreciated species that yet play crucial roles in ecosystem functioning.