Palaeontological animal bone deposits are rarely investigated through research partnerships where the local First Nations communities have a defining hand in both the research questions asked and the research processes. Here we report research undertaken through such a partnership approach at the iconic archaeological site of Cloggs Cave (GunaiKurnai Country, East Gippsland), in the southern foothills of SE Australia’s Great Dividing Range. A new excavation was combined with detailed chronometric dating, high-resolution 3D mapping, and geomorphological studies. This allowed for the interpretation of a sequence of stratigraphic layers spanning from a lowermost excavated mixed layer dated to between 25,640–48,470 cal BP, to a dense set of uppermost, ash layers dated to between 1460–3360 cal BP. This long and well-dated chronostratigraphic sequence enabled temporal trends in the abundant small mammal remains to be examined. The fossil assemblage consists of at least 31 taxa of mammals which change in proportions through time. Despite clear evidence that the Old Ancestors repeatedly carried vegetation into the cave to fuel cool fires (no visible vegetation grows in Cloggs Cave), we observed little to no evidence of cooking fires or calcined bone, suggesting that people had little involvement with the accumulation of the faunal remains. Small mammal bones were most likely deposited in the cave by large disc-faced owls, Tyto novaehollandae (Masked Owl) or Tyto tenebricosa (Sooty Owl). Despite being well-dated and largely undisturbed, the Cloggs Cave assemblage does not appear to track known Late Quaternary environmental change. Instead, the complex geomorphology of the area fostered a vegetation mosaic that supported mammals with divergent habitat preferences. The faunal deposit suggests a local ancestral landscape characterised by a resilient mosaic of habitats that persisted over thousands of years, signaling that the Old Ancestors burned landscape fires to encourage and manage patches of different vegetation types and ages within and through periods of climate change.