Fragmentation impacts species composition in the forests by decreasing species richness, affecting species interactions essential for plant reproduction and forest maintenance. To understand fragmentation effects on plant-animal interactions, we assessed how the characteristics of a fragmented landscape influence an interaction network between frugivorous bats and plants in tropical forest remnants. We captured bats using mist nets and analyzed the seeds found in their feces to record their interaction with plants in 10 remnants of tropical dry forests (TDF) in Colombia. We then calculated landscape metrics for each remnant at different spatial scales to assess the effects of fragmentation on the interaction network properties of remnants. Additionally, we employed a multilayer interaction network approach to examine the spatial variation in bat-plant interactions across remnants. We captured 1142 bats representing 36 species and collected more than 19600 seeds from their feces, demonstrating bats’ vital role in seed dispersal and tropical dry forest health. We found higher levels of nestedness in smaller and more isolated remnants, suggesting a loss of specialist interactions and a shift toward more generalized associations. In contrast, modularity levels remained unaffected across remnants, likely due to the flexible nature of species interactions at different sites. The multilayer network indicates that plants and bats exhibited flexibility in their interactions across remnants, with plants showing greater variation than bats. This flexibility indicates species can adopt different functional roles depending on local remnant conditions. Results suggest that habitat fragmentation can disrupt the structure of ecological networks by reducing specialist interactions and promoting more generalized associations, leading to a loss of ecological complexity. Thus, maintaining large, heterogeneous, and less fragmented habitats is key to sustaining both bat and plant populations and the integrity of their mutualistic networks.