This data article is about bats observed from fragmented forest understories interspaced by agricultural plantations, utility corridors, and man-made structures within rural areas of Setiu (Bukit Kesing Forest Reserve and Ladang Tayor TDM) and Hulu Terengganu (Pengkalan Utama and Sungai Buweh, Kenyir) that are situated in Terengganu state, Peninsular Malaysia. Surveys were conducted from October 2018 until January 2019. These bats were captured using harp traps and mist nets that were set 30 m apart across flyways, streams, rivers and less cluttered trees in the 50 m transect zones (identified at each site). All animals captured were distinguished by morphology and released at the same location it was caught. The data comprise of 15 species of bats from four family groups, namely Hipposideridae, Pteropodidae, Rhinolophidae and Vespertilionidae. The data were interpreted into weight-forearm length (W-FA) to inform about bats Body Condition Index (-0.25 to 0.25).