Bats are often associated with several zoonotic diseases, including helminth infections. Despite their potential detrimental effects on both human and bat populations, information on helminth parasites of Philippine bats remains scarce. Here, we identify gastrointestinal helminths parasitizing bats collected from a cave complex in Cavinti, Laguna Province, Philippines, determine their prevalence (P) and mean intensity (MI), and investigate relationship of helminth prevalence and intensity with bat host characteristics including sex, diet, age, and roosting habit. We isolated 581 individuals of helminths representing six taxa (three trematodes, two nematodes, one cestode) from the gastrointestinal tract of sampled bats. Helminths were observed in 82 out of 172 bats captured (P = 47.67%), with Miniopteruspaululus having the highest infection rate (P = 91.3%) and highest MI (18 ± 4.5/infected bat). Helminths parasitizing endemic bat species from the Philippines, such as Rhinolophus rufus, Rhinolophus inops, Hipposideros pygmaeus, and Ptenochirus jagori were reported here for the first time. We provide new host records for other helminth species and report the presence of two parasites, Plagiorchis sp. and Toxocara sp., known for their zoonotic potential. These data will contribute to efforts in identifying parasites and diseases harbored by bats in the country and develop additional conservation measures for bats.