The Large-eared Flying Fox has been recorded from a wide range of lowland habitat types including both primary and secondary tropical moist forest, monsoon forest, dry forest, savanna woodland, swamp forest, coconut and sago plantations, and  subsistence gardens (Flannery 1995a,b; Bonaccorso 1998). It is common in coastal mangroves in the Kikori River delta of Papua New Guinea, and is often mist-netted flying along creek-lines (T. Leary pers. comm.). Animals are relatively placid to handle, compared with other species of flying-fox (T. Leary pers. comm.).

Little is known of roosting behaviour, although animals have been observed roosting singularly or in pairs on four occasions in the mangroves of the Kikori River (T. Leary pers. comm.).  Hall (2008) describes a mixed species camp of Pteropus scapulatus and P. macrotis on Boigu Island and also describes “large numbers” of animals flying from the island to the Papua New Guinea coast just 12 kilometres away. In the camp in Torres Strait bats hung at all levels from the canopy to branches that are submerged at high tide (Hall 2008). However animals observed roosting in PNG mangroves were all in the lower- to mid-canopy, in locations which afforded good overhead cover (T. Leary pers. comm.).

Very little is known about the reproduction of this species, but there are indications that at least in some parts of its range births may occur between September and December (Bonaccorso 1998, T. Leary pers. obs.). A  juvenile born in captivity was weaned from its mother 184 days after birth (Bonaccorso 1998). Other Pteropus species give birth to a single young per year.

This species is listed on Appendix II of CITES, but is unlikely to be traded internationally. It occurs in several protected areas. The impacts of hunting on this species need further study. Bonaccorso (1998) recommends population surveys and natural history studies be undertaken and the species potential vulnerability to hunting be assessed.