It occurs in lowland tropical forest. A colony was found in a mangrove forest in Seram, though individuals were also found in patchy forests near villages (Tsang et al. 2015). In Seram, the species has been sighted feeding on flowers of durian trees (Durio sp.), but more research is needed to understand their feeding ecology (Tsang et al. 2015).

This species is endemic to the central Moluccas (Seram, Buru) and adjacent small islands in Indonesia. It is also present in Tanimbar (also called Timor Laut) island groups. It is likely now absent from Ambon. Pending further review, Pteropus melanopogon do not occur on the Kai and Aru Islands, as those species are now recognition as separate species (Pteropus keyensis on the Kai Islands and Pteropus aruensis on the Aru Islands).

This species is listed on Appendix II of CITES. This species possibly occurs in protected areas. The only presently recorded colony from Seram does not have any level of protection (Tsang et al. 2015). Further research is needed to resolve the taxonomy of this species, and to determine the current population status, habitats, feeding ecology, and the impact of present hunting levels.