The Kiowa rockshelter (Simbu province, Papua New Guinea) was first excavated in 1964 by a team led by Susan Bulmer. Located at around 1530 meters above sea level (masl) this rockshelter was used from the late Pleistocene to late-Holocene (12 k to 3 kya). Lithic assemblages and faunal remains excavated at Kiowa suggest that the site was first used as a hunting camp, with bats being the species most frequently captured. This led to the large fruit bat (Aproteles bulmerae) becoming locally extinct around 10 kya, although found to be extant elsewhere in New Guinea. The aim of this work is to propose a methodological approach to access data from A. bulmerae remains. Mandible fragments from A. bulmerae were sent from the University of Papua New Guinea to CNRS Toulouse where they were subjected to a series of analyses. First, the samples were scanned using an X-ray micro-tomographic instrument (Phoenix Nanotom 180) as a non-destructive technique to record digital 3-D morphological data. Second, samples were screened to assess the amount of collagen present using Fourier transform infrared spectroscopy (FTIR), and samples with enough collagen (>3%) were selected for direct 14C dating. Finally, DNA extraction and shotgun analysis retrieved <1% of endogenous DNA from some samples. Further analyses are carried out to determine whether future phylogenetic analysis could be performed from these aDNA data. Our study demonstrates that a step-by-step methodological approach can maximize data recovery and limit the destruction of valuable archaeological material. Moreover, we show that organic matter can be retrieved from biological remains from the New Guinea Highlands for dating and DNA analysis, opening new research perspectives to study human (pre)history in this region.