The spectacled flying fox was listed as a threatened species under the Environment Protection and Biodiversity Conservation Act 1999.

They were considered vulnerable due to a significant decline in numbers as a result of loss of their prime feeding habitat and secluded camp sites.

It has also been reported that spectacled flying foxes skim over the surface of water to drink and are sometimes eaten by crocodiles.

[1] In February 2019, the Australian government upgraded the threatened status from vulnerable to endangered, after almost a third of the bat population died in a severe heatwave in Queensland in late 2018.

Natural causes of mortality include predation mainly by rufous owls, Freshwater crocodiles, and olive pythons, death by paralysis tick when bats climb low to the ground to feed, and the death of babies that are born too early when either something goes wrong in the fetus' development, or the mother suffers from prolonged stress.

Flying foxes are also frequently killed in human-related incidents such as landing on power lines, and getting entangled in nets or barbed wire.

In February 2019, the Australian Department of the Environment and Energy announced that the national status of the spectacled flying fox was going to be revised from vulnerable to endangered.