The Temotu Flying Fox forages in mangroves, primary  and secondary forest, subsistence gardens / agroforests and coconut plantations. Pteropus nitendiensis is frequently observed foraging during the daylight hours, with activity peaking in mid to late afternoon (T. Leary, C. Posala and R. Pierce pers. comm). The Temotu Flying Fox predominantly roosts singularly or in pairs (T. Leary, C. Posala and R. Pierce pers. comm). It has primarily been observed roosting in the lower-mid levels of the canopy, in positions that offered overhead cover.

A diverse assemblage of plants that provide food in the form of fruits, flowers and nectar, or leaves have been documented (Leary and Aujare 1994; T. Leary, C. Posala and R. Pierce pers. comm). There is little information on the reproduction of the species and it is unknown if breeding is seasonal. A single pregnant female was collected in early September 1990 (Flannery 1995; T. Leary unpublished data), a lactating female was caught in October 1993, and several females carrying a single young were observed in November 1993 (Leary and Aujuare 1994). In recent surveys, a local informant reported observing a female with a large young attached in August 2015 (T. Leary pers. comm). In April 2018 P. nitendiensis were repeatedly encountered roosting in pairs, and informants relayed that these were male and female mating pairs (C. Posala pers. comm). Other Pteropus species bear a single young, gestation is around six months, and have a lifespan that is approximately 8 or 9 years.

This species is known only from the islands of Nendö, and two smaller islands less than 2 km away Temotu Nöi and Malö, collectively known as Nendö or Santa Cruz in the southern Solomon Islands (Leary and Aujare 1994, Flannery 1995), It has recently been recorded at low density on Tinakula Island, an active volcano (~8 km² and less than 40 km to the north-east of Nendö) (T. Leary, and R. Pierce pers. obs). The total area of these islands is around 551 km² and if the species does not occur at higher altitudes the area of occupancy would be roughly 443 km². It has one of the most restricted ranges of Pteropus in the Solomon Islands (Leary and Aujare 1994).

Although all Pteropus are listed on Appendix II of CITES it is highly unlikely that the species is traded internationally. Pteropus nitendiensis is not present in any protected areas. Further survey is needed at a wider range of habitat types and elevations, particularly elevations above 200 m and away from the coastal strip where cultivated food trees are abundant and may, at least seasonally support higher densities of the species. Surveys should include seasonal monitoring of population trends in a wide range of habitats and elevations. Further research is needed on habitat use to determine the suitability of logged forests since logging is ongoing and further re-entry logging on less than a 35-year rotation is proposed/occurring on Nendö.