Human disturbances have reduced the three basic niche dimensions for the survival of some mammalian species (space, time, and resources). Anthropic activities cause the extinction of ecological functionalities faster than species extinctions. In this study, we identified four types of habitats in the Ecuadorian Andean Chocó: primary forest (PF), secondary forest in natural regeneration (SF1), secondary forest in assisted regeneration (SF2), and pastures for cattle (P). The main objective was to determine the responses in the trophic niche and the ecological relationships of understory phyllostomid bat communities. We captured bats with mist nets and obtained fecal samples from 21 species. These were analyzed to quantify seeds, pollen, insects, and vertebrates consumed by each individual, with counts organized by species and habitat type. We conducted an ecological relationship analysis to understand the structure of bat–fruit networks and their dietary preferences. We calculated niche breadth and niche overlap to understand the trophic niche composition of each species. We applied null models to evaluate if there is evidence of trophic niche partitioning among these species. Despite a relatively small sample size, the results obtained are nevertheless interesting. While niche breadth was not useful for detecting the effects of human disturbances, niche overlap was significantly higher in disturbed habitats (SF1, SF2 and P), where ecological relationships were weaker. Most of the species were related to the consumption of seeds from the genus Piper. These results indicate that bat communities and their ecosystem services may be highly endangered due to anthropogenic disturbances. Network interactions in bats are highly variable in geographic space and time, and little is known about the community structure of bat–seed interactions. Studying mutualistic networks in bats and seeds is crucial because of their role in ecosystem support, supply, and regulation services that depend on them.