Ptenochirus minor is found in lowland and montane forest and secondary forest (Heaney et al. 1998, 2010); it does not occur in agricultural or urban areas (L. Heaney pers. comm. 2006). It apparently coexists at upper elevations with P. jagori (L. Heaney pers. comm. 2006). In a 2002 mist net survey on Mount Apo, Mindanao, Ptenochirus minor was uncommon in lower elevation mossy-montane forest that had been subjected to habitat alteration (Jakosalem et al. unpublished report). Lactating females were observed in August in Leyte (M.R. Duya pers comm).

The Lesser Musky Fruit Bat is endemic to the Philippines, where it is found only in the Mindanao faunal region. Records are from Biliran, Bohol (R. Pamaong pers. comm. 2006), Dinagat, Leyte, Mindanao (Agusan del Norte, Agusan del Sur, Bukidnon, Compostela Valley, Cotabato, Davao del Sur, Misamis Occidental, South Cotabato, Sultan Kudarat, and Surigao del Sur provinces, though it probably occurs throughout the island (L. Heaney pers. comm.), Leyte (Fidelino et al. 2020) and Samar (J.C. Gonzalez pers. comm. 2006, R. Gomez pers. comm. 2007) (Yoshiyuki 1979, Heaney et al. 1998, Heaney et al. 2010). A record from Palawan (Yoshiyuki 1979) is almost certainly erroneous (L. Heaney pers. comm. 2006). It has been recorded from sea level to 1,600 m asl.

Ptenochirus minor occurs in some protected areas. Additional research is needed on its population status and trends, and threats.