This bat is usually found roosting in rock fissures and caves (MacKinnon et al. 2003) although it may also roost in tree foliage. In the Ankarana National Park it often roosted in high points near the large entrances of long caves with a high buffering capacity for temperature and relative humidity (Cardiff 2006). The species' patchy distribution, which includes humid, dry deciduous and spiny forest, is probably related to the availability of suitable roost sites and E. dupreanum is rare or absent from a number of forests without rocky outcrops (Goodman et al. 2005, Schmid and Alonso 2005, Jenkins et al. 2007). Although it continues to survive in highly modified landscapes with very little native vegetation remaining (Ratrimomanarivo 2007), it appears to use native forest vegetation for food in preference to introduced plants (Picot et al. 2007).

Fruit is the main dietary component but it also eats leaves and other plant parts (Picot 2005, Picot et al. 2007). Through the ingestion of nectar and small seeds, a significant role in pollination and seed dispersal is inferred (Picot et al. 2007, Ratrimomanarivo 2007). Plants are often found growing out of the faeces beneath rock crevices occupied by E. dupreanum (P.A. Racey, unpublished), which is also an important pollinator of threatened baobab trees (Baum 1995, Andriafidison et al. 2006).

MacKinnon et al. (2003) suggested that E. dupreanum might be migratory (like its congener in Africa, Richter and Cumming, 2008) because of regular variation in the occupancy and abundance of roosts. Antibodies to Nipah, Hendra, and Lagos Bat viruses, and isolates of other viruses were detected in E. dupreanum at several sites in Madasgascar (Iehlé et al. 2007, Razafindratsimandresy et al. 2009, Reynes et al. 2011). Additional research is needed on natural history and in particular roosting ecology and movements.

This species is endemic to the island of Madagascar where it is widespread, albeit with a patchy distribution (MacKinnon et al. 2003). It is found in coastal areas and on the central high plateau, although absence of records probably reflects inadequate survey coverage rather than a genuine absence. There are some areas within its range where the lack of suitable rock formations means there are no roosting opportunities (Goodman et al. 2005).

This species is known from a number of protected areas (Goodman et al. 2005) including, Parcs National d’Isalo, Namoroka, Ankarana and Tsingy de Bemaraha, and Réserve Spéciale de Cap Sainte Marie, however, hunting has been reported from within the Parc National d’Ankarana (Cardiff et al. 2009). Roosts that are located in inaccessible rock outcrops, in caves with high entrances, or sites that are further from accessible savannah appear to be relatively protected (Cardiff et al. 2009). Cave roosts are probably subject to highest hunting pressure and conservation measures should be focused at these sites.