The transition from foraging cultures to more socially complex agricultural communities has been a subject of great interest across the globe. Both socio-political and population density factors have been proposed in many regions including Island Southeast Asia where Neolithic and then Metal-Age cultures appear to have dispersed rapidly along highly inter-connected maritime networks after 4000 BP. Recent excavations at two cave sites, Nana Bici Acin and Atu Gua Luli, situated 30 km inland from the Timor coast on the Koleki ridge near Maliana in Timor-Leste provide an opportunity to investigate how inland montane regions of depauperate Wallacea were accessed by people connected to these networks. Our research aims were to demonstrate human adaptations to terrestrial montane landscapes during these Neolithic and Metal-Age cultural transitions. Atu Gua Luli saw settlements as far back as ca. 6800 cal. BP, spanning the transition from preceramic to Neolithic and later Metal-Age cultures. Concentrated chert assemblages were recorded, as were vertebrate and invertebrate remains that indicate broad spectrum foraging for protein resources in aquatic and forest environments. By the beginning of the Neolithic period c. 3800 cal. BP, human activity appears more intensive with a greater abundance of fire activity and lithic deposition coinciding with the appearance of pottery and domesticates that indicates both Austronesian and Austroasiatic influences. The Metal-Age period ca. 2500 BP, as represented by glass beads and the disappearance of giant rats, saw a decline in human cave use. The presence of red-slipped and Metal-Age pottery, marine fish, shellfish, and shell-disc beads, at Koleki and other sites in Timor-Leste, indicates continuous connections between inland and coastal socio-political networks in the region during the period leading up to and spanning the Neolithic and Metal-Age transitions.