This species is found in rainforest, savanna forest, and dry open areas. It roosts in caves and overhangs, mines, old buildings, culverts under roads, and tree hollows (Bonaccorso 1998; Hall 2008). In Australia, it apparently uses the thin strips of rainforest vegetation in riparian zones of major rivers to move out from larger patches of occupied rainforest habitat (K.N. Armstrong unpublished obs.). It is not known to form larger roosting aggregations like other hipposiderids species, instead roosting singly or in small groups of up to ten individuals (Hall 2008). Females give birth to single young around November (Churchill 2008). Females are larger and produce echolocation calls with a lower frequency compared to males. Generation length is around 6–7 years (Woinarski et al. 2014).

The presence of H. semoni in Papua New Guinea is represented by museum specimens from near Vanimo in Sandaun (West Sepik) Province, localities in Morobe Province, and several localities around Port Moresby. Given the intactness of much of the habitat in Papua New Guinea, it might have a broad distribution, though occur at low density given that numerous surveys in recent years in several provinces have not produced captures. Acoustic detection in Papua New Guinea, the most efficient way to assess area of occupancy, is hindered by a lack of information on the similarity of its call to other closely related New Guinea Hipposideros (K.N. Armstrong and K.P. Aplin unpublished data). In Australia, the majority of recent records are from the eastern side of Cape York Peninsula, Queensland—Iron Range, Kulla, Oyala Thumotang and Cape Melville National Parks, near Cooktown and south to Townsville (Reardon et al. 2010; Woinarski et al. 2014). There is also a single report of a disjunct occurrence ca 700 km further south in Kroombit Tops National Park (south of Gladstone, Queensland; Schulz and de Oliveira 1995), and an unconfirmed and likely erroneous acoustic record as far south as Maryborough (de Oliveira and Pavey 1995; probably from Rhinolophus megaphyllus). It ranges from sea level such as at Cape Melville National Park, Queensland to over 1,400 m Asl in Morobe Province, Papua New Guinea.

A Recovery Plan has been developed for Hipposideros semoni in Australia (Thomson et al. 2001). It is found in several protected areas in Queensland, and is listed under national environmental legislation in Australia as a threatened species. Taxonomic studies need to be completed, and further studies are needed into the distribution (particularly within New Guinea), abundance, natural history, and threats to this species.