Hipposideros wollastoni has been reported from a wide variety of primary forest habitats throughout its elevational range, including Montane Nothofagus forest, oak forest habitats between 1,400 and 1,600 m Asl and Hill Forest at lower elevations, as well as secondary forest.  It roosts in caves, often with high humidity or water, and this thus associated with limestone landscape units. 

This species is restricted to the island of New Guinea. In Papua Province, Indonesia it has been recorded from the Utakwas River, Fak-fak District (the nominate subspecies H. w. wollastoni; Flannery 1995; Bonaccorso 1998). In Papua New Guinea most records (H. wollastoni parnabyi) in the last century were from the central cordillera in Western and Sandaun (West Sepik) provinces, predominantly around Telefomin and Tifalmin, and one locality in Gulf Province (Bonaccorso 1998). The third subspecies H. w. fasensis has only been found in the North Coastal Ranges in northern Sandaun Province (Flannery and Colgan 1993). In the past two decades there have been additional captures and acoustic records from elsewhere in Western, Sandaun and Gulf provinces, contributing to knowledge of area of occupancy, as well as Chimbu, Southern Highlands and Morobe provinces that extend its known range (Leary 2004; Armstrong and Aplin 2011; Armstrong et al. 2015; K.P. Aplin and K.N. Armstrong unpublished data; D. Wright pers. comm.), but it was not recorded in Western Highlands Province or on the Huon Peninsula (Robson et al. 2012; Armstrong and Aplin 2014). It ranges between 30 and 2,440 m Asl (Bonaccorso 1998; Armstrong et al. 2015). 

Protection of known roosting sites and of habitat in general within wildlife management areas will help conservation of H. wollastoni. Further studies into the distribution, ecology, and threats to this species are needed.