The habitat is poorly known but the species has been mostly recorded from dry and arid savanna habitats, with deciduous bushland and thickets dominated by Acacia and Commiphora (usually near rivers and/or highlands) (Kityo and Kerbis 1996, Happold 2013). It is possible that this species has a specialised diet to persist in its arid habitat (Mickleburgh et al. 2008). However, the species may also inhabit afromontane vegetation on the slopes of Kenyan and Ethiopian highlands (Happold 2013).

The East African Epauletted Fruit Bat is a dry low altitude savanna species that may be sympatric with E. labiatus (Thorn and Kerbis Peterhans 2009, Happold 2013). The species occurs in isolated population ranges in the dry savanna and rocky areas of its range in Ethiopia, Somalia, Kenya and northernmost Tanzania, and Uganda. Specifically, isolated population ranges in central Ethiopia, central, northern and eastern Kenya, and Somalia (Aggundey and Schlitter 1984, Claessen and De Vree 1991, Happold 2013), northernmost Tanzania and in northern and western Uganda (Kityo and Kerbis 1996, Patterson and Webala 2012).

It is not known if the species is present in any protected areas, some individuals have been captured at Lake Bogoria National Reserve, Kenya (Wechuli et al. unpublished data). Further studies are needed into the distribution, natural history and possible threats to this species.