This species has been recorded from primary and secondary tropical moist forest and coral rag forest. Roosting take place in trees. In addition to native plants the bats also feed on cultivated fruits and are considered a minor nuisance in some areas. It is considered to be an important dispersal agent for some of the native forest trees, including some rare endemics (Gerlach 2004).

This species is has been recorded from the Seychelles, the Union of the Comoro and Tanzania. In the Seychelles it is present on a number of islands including Mahé, Praslin, La Digue, and Silhouette. Gerlach (2004) mentions that it has recently been recorded roosting on a number of islands where its presence was previously unconfirmed. In the Comoros it is known from the islands of Anjouan, Grand Comore and Moheli. In Tanzania, it is restricted to Mafia island.

A large population (2,000 to 3,000 bats) of this species is present in the Morne Seychellois National Park on Mahé, Seychelles (Nicholl and Racey 1981). There is a general need to continue monitoring activities for this species in order to detect any possible declines and to determine if there are any movements between populations. Studies are underway to better determine the taxonomic status of the population of bats from Mafia Island (Pteropus seychellensis comorensis) largely to understand if this population should be recognised at the species level distinct from P. seychellensis. The population of Mafia Island may be threatened, and an assessment of the situation on this island and of the possibilities for the species’ protection there is highly desirable (Mickleburgh et al. 1992).
This species is listed on Appendix II of CITES.