Bats are considered important reservoirs of pathogens of veterinary and medical relevance worldwide. However, despite the increasing attention paid towards the central role of bats in the spreading of some zoonotic infections, studies on their own parasites remain patchy especially in Neotropical regions. Understanding the relationships occurring between bats and their pathogens is a crucial step to determine the implications undermining the ecology and biology of these animals. The present study aims to assess the endoparasitic fauna of Neotropical bats from Northeastern Brazil, with a particular focus on helminths and protozoa. From October 2016 to March 2017, 54 fresh faecal samples were collected in stable shelters inhabited by three different bat species (i.e., Molossus molossus, Myotis lavali and Noctilio albiventris). Samples were analysed using four different techniques (i.e., Centrifugal Sedimentation, Flotation Technique, Spontaneous Sedimentation Technique and FLOTAC®). A total of 96.29% (52/54) samples were positive for at least one gastrointestinal parasite and 11 different families were identified. In particular, 63.6% (7/11) of the families were of helminths and 36.4% (4/11) of protozoa. Helminths were classified into two different classes (Nematoda and Cestoda) and seven families, whereas the four protozoa classes detected (i.e., Coccidia, Gregarinomorphe, Lobosea and Zoomastigophora) into four families. Eggs of Ancylostomatidae and Hymenolepididae were the most abundan. The findings of this present study demonstrate that Neotropical bats from Northeastern Brazil are parasitized by a wide number of parasites, and some of them may have important implications for Public Health.