The Philippine Pygmy Fruit Bat inhabits lowland and montane, ultramafic forest (Duya et al. 2020) primary and secondary habitats, including mossy forest, and mixed agricultural habitats and second-growth forest and old reforestation areas (Fidelino et al. 2020). It exhibits an 8- month delay in embryo development which gives a gestation period of 11.5 months, the longest known in bats (Heideman 1989). Females can become pregnant at the age of three to five months (Heideman 1989). The species is an important seed distributor.

Haplonycteris fischeri is endemic to the Philippines. It is widespread through most of the country, excluding the Camiguin, Palawan, and Batanes/Babuyan faunal regions. It has been recorded from Biliran, Bohol, Catanduanes, Cebu (Cebu Cloud Forest Reserve) Dinagat, Leyte, Luzon (Albay, Aurora, Bataan, Cagayan, Camarines Sur, Isabela, Laguna, Quezon, Quirino, Tarlac, and Zambales provinces), Marinduque, Mindanao (Agusan del Norte, Bukidnon, Davao del Norte, Davao del Sur, Davao Oriental, Lanao del Norte (R. Pamaong pers. comm. 2006), Misamis Occidental, Misamis Oriental, South Cotabato, Surigao del Norte, Surigao del Sur, Zamboanga del Norte, and Zamboanga del Sur provinces), Mindoro, Negros, Panay, Palaui, and Samar (J.C. Gonzalez pers. comm. 2006) (Heaney et al. 1998). The record from Palawan reported by Kock (1969) is probably erroneous, which is supported by recent failure to record this species on Palawan Island despite extensive netting there (Esselstyn et al. 2004, L. Heaney pers. comm. 2006). Records are from 150–2,250 m (Heaney et al. 1998).

Haplonycteris fischeri occurs in a number of protected areas. Additional research is needed on the species distribution, population status and trends, and threats.