The habitat and ecology of this species is virtually unknown, except that they have been recorded to roost in coconut palms (Haribon Project unpublished data). It is likely to be associated with lowland forests, but more research is needed on its habitat preferences. The recently recorded population in Panglima Sugala (Tawi-tawi) is in the middle of town.

This species is found in the Philippines and Indonesia. In the Philippines, it is reported from Mt. Matumtum in southern Mindanao (Paguntalan unpublished data 2018), Basilan, Malanipa, the tip of the Zamboanga peninsula on Mindanao (Zamboanga del Sur Province), as well as Sanga-sanga, Sibutu, and Tawi-tawi in the Sulu Islands (Heaney et al. 1998). The species was most recently caught in the Turtle Islands and colonies in Panglima Sugala (Tawi-tawi) resemble the verified P. speciosus from the Turtle Islands. There is potentially another colony in Bonggao that requires verification (Paguntalan unpublished data 2018). The species is also known from two small islands in Indonesia, off the southeast coast of Borneo, Masalambu Besar (Solombo Besar) and Mata Siri (Java Sea), and from Karakelong in the Talaud Islands (Simmons 2005). Previous reports from Cebu, Mactan, and Negros in the Philippines were based on subadult Pteropus hypomelanus (Heaney et al. 1998). All reports of the species are from low elevations, up to 800 m asl.

This species is listed on Appendix II of CITES. In the Philippines, the Wildlife Conservation and Protection Act (Republic Act 9147, approved into law in 2004) confers protection to flying foxes. The National Integrated Protected Areas System (Republic Act 7586) and the Expanded National Integrated Protected Areas in the Philippines (Republic Act 11038) also confers protection to flying foxes inside protected areas. In 1996, the Turtle Islands were declared the Turtle Islands Heritage protected area by both the Philippine and Malaysian governments in recognizing it is one of the few major nesting grounds for green turtles left in the world, and only scientific and conservation activities are allowed under the supervision of the government. However, the impact this has on protection of terrestrial fauna such as flying foxes is unknown. Further studies are needed into the taxonomy, distribution, abundance, natural history and threats to this species.