This largely coastal species is found in areas of mangrove and swamp forest, and in tropical moist forest and in savannas near water (Loughland 1998, Bonaccorso 1998, Churchill 2008), it is also found in urban environments (Markus et al. 2008). It roosts in large colonies of several hundred to tens of thousands of animals (Bonaccorso 1998, Welbergen 2008) in patches of trees and dense vegetation, and can form mixed-species colonies with other flying fox species including P. scapulatus, P. poliocephalus, P. conspicillatus, P. neohibernicus, and Acerodon celebensis. There is one exception of P. alecto roosting in a natural limestone tower in northern Australia (Chillego, Stager and Hall 1983). In northern Queensland where both P. alecto and P. conspicillatus occur, they are typically not recorded at the same roost (Churchill 2008). However, small groups have been observed co-roosting at a limited number of sites, e.g. Ingham, Cairns and Finch Hatton (Parson et al. 2010, J. Welbergen pers. comm.). In Sulawesi, P. alecto are typically found co-roosting with Acerodon celebensis (S.M. Tsang and S. Wiantoro pers. comm.).

Pteropus alecto is capable of long-distance movements, with cumulative movements of hundreds of kilometers within a year, including across international boundaries and transversing significant distances across the sea(Breed et al. 2010). For example, using satellite telemetry, P. alecto was recorded transiting the Torres Strait between Australia and Papua New Guinea (Western Provience), a distance of 150 km and moving between Papua New Guinea and Indonesia (Breed et al. 2010). Nightly movements of >60 km between roosts (J. Welbergen pers. comm.) and distances of up to 220 km in two days between roosts (B. Roberts pers comm.) have been recorded. In Papua New Guinea camps range in size from several hundred to up to 3,000, and their locations may shift frequently with many camps not present from one year to the next (A. Breed and T. Leary pers. comm).

However, the movement patterns of P. alecto vary between individuals, while some move long distances, others remain relatively sedentary. Some individual P. alecto can adopt a primarily sedentary lifestyle in areas where a high diversity of food plants provide a continuous food supply (Markus 2001, Breed et al. 2010).

The primary food source in Australia is the flowers of Eucalyptus, Banksia, Melaleuca species, plus rainforest and exotic fruits (Markus and Hall 2004). Using radio-tracking individual animals were shown to move a total of 26 km during nightly feeding in urban Brisbane. Using satellite telemetry, nightly movements of 32 km between feeding sites and roosts have been recorded (B. Roberts pers. comm.). P. alecto can maintain fidelity to feeding sites for an average of one month, although considerable variation is likely (McWilliams 1986). A study in northern Australia found that the feeding distances of P. alecto changed seasonally, with individuals travelling further during the dry season when feeding on Eucalyptus species compared with the wet season when feeding on locally abundant rainforest fruit (Palmer 1997, Palmer and Woinarski 1999). Some variation between movements of male and females P. alecto has been reported, with lactating females traveling greater distances between roosts and foraging sites than males (Palmer and Woinarski 1999).

Pregnancy in P. alecto lasts for 27 weeks (Martin et al. 1996) and females annually give birth to a single young. In northern Australia at 12ºS most births occur between January and March, in contrast to October and November at 27ºS in eastern Australia (Vardon and Tidemann 1998). However, a small proportion of young are born outside the major birth peaks in both areas (Vardon and Tidemann 1998). The timing of reproduction may vary according to the seasonal abundance of regional food resources (Vardon and Tidemann 1998).

Pteropus alecto is common in coastal subtropical and tropical northern and eastern Australia, from Shark Bay In Western Australia to south-eastern New South Wales (Hall and Richards 2000, Churchill 2008). It is also found through the Torres Strait including Poruma, Warraber and Boigu Island (Helgen 2004, Lavery et al. 2012), in parts of southern New Guinea including the coastal plain of the Western, Gulf and Central Provinces until the Yule Islands (Bonaccorso 1998, A. Breed and T. Leary pers. comm.), and the Indonesian islands of Sulawesi, Salayar, Sumba and Sava (Breed et al. 2013, A. Breed pers comm.). In northern Australia, P. alecto has been found as far as 250 km inland (Thompson1991), but typically occurs in coastal areas (Hall and Richards 2000). Over the past century, P. alecto has expanded its southern range limit by approximately 10.5 degrees latitude from Rochamption, Queensland to Wollongong, New South Wales (Roberts et al. 2012a, J. Martin pers. comm.), with single (vagrant) individuals reported as far south as Melbourne, Victoria, and Adelaide, South Australia.

The species was previously reported in eastern Java, Lombok and the Kangean islands, however, recent information suggests that P. alecto have not been confirmed in these locations in recent decades (A. Breed pers comm.). Previously collected specimens from Timor that were thought to be P. alecto were indicated to be P. vampyrus according to mtDNA sequence analysis (A. Breed pers. comm.).

This species is listed on Appendix II of CITES. Some roosting and feeding habitats are in protected areas, but a very small proportion of the population is likely to occur in protected areas at any time.

An unknown proportion of the population in eastern Australia has been monitored in State and National Flying-fox monitoring programs since mid-2007.

Lethal crop protection is regulated in eastern Australia.