This data article informs about Chiropteran diversity, new records, ecosystem services and possible pathogen carriers in fragmented forests (sub-divided by utility corridors, man-made structures, untouched and secondary plantations) within districts Setiu (Setiu Research Station), Hulu Terengganu (Saok and Lasir waterfalls) and Besut (Gunung Tebu Forest Reserve) of state Terengganu, Peninsular Malaysia. These bats were captured using harp traps and mist nets that were set 10 m apart across flyways, streams and less cluttered trees in the 50 m × 50 m transect zones (identified at each site). All animals were distinguished by morphology and gender before their release at the site of capture. The data comprise of five bat family groups Hipposideridae, Megadermatidae, Pteropodidae, Rhinolophidae and Vespertilionidae. It is interesting to note that untouched Saok Waterfalls is home to wide variety of bats listed (68.8%), followed by secondary forests of Gunung Tebu Forest Reserve (24.8%), untouched Lasir Waterfalls (4.8%) and lastly, Setiu Research Station as least favored (1.6%). Chiroptera like Cynopterus brachyotis (n = 23, 37.7%), Hipposideros bicolor (n = 6, 9.8%) and Scotophilus kuhli (n = 6, 9.8%) were most dominant in the checklist whereas Hipposideros armiger, Murina suilla and Scotophilus kuhlii are new data records in the fragmented forests of Terengganu. The data were interpret into Shannon, Simpson, Margalef, Menhinik and Evenness indices to individually or collectively distinguish chiropteran variety in Terengganu State whereas weight-forearm length (W/FA) informs about chiropteran Body Condition Index (-0.25 to 0.25). The function of bats were also identified to distinguish service providers (pollination and forests regeneration) and zoonotic pathogen carriers (in particular to Leptospira bacteria, Nipah virus and Sindbis virus).