Caves are characterized by unique abiotic conditions such as limited light, and they therefore support distinct faunal assemblages that often include endemic species. Due to light limitations, photoautotrophic organisms are absent from many subterranean food-webs, which therefore predominantly rely on allochthonous nutrient sources. For this reason, hypogean habitats are expected to display lower assemblage diversity than that seen in epigean ecosystems. Bat guano, a major source of allochthonous nutrients in caves, varies substantially in composition based on its origin—whether it is produced by frugivorous or by insectivorous bats—and on its deposition site within the cave. This study examines how allochthonous nutrient sources and zones within caves influence arthropod diversity and assemblage composition. We found that both the type of allochthonous nutrient source and cave characteristics strongly affect the composition of arthropod assemblages. Our results show that caves harboring frugivorous bat colonies have a lower abundance of flies than caves with either insectivorous bat colonies or no bat colonies. Moreover, caves without bat colonies were seen to have low species richness of both detritivores and predators compared to caves housing either frugivorous or insectivorous bats. Additionally, species diversity and assemblage composition differed substantially between the twilight and dark zones of the caves. These findings demonstrate that allochthonous nutrient sources, the ecological zone, and the microhabitat within the cave are key drivers of arthropod assemblage composition and diversity. This study advances our understanding of cave ecology and underscores the importance of conserving diverse cave types for protecting their unique arthropod diversity.