Land-use change is a major driver of biodiversity loss. Large-scale disturbances such as habitat loss, fragmentation and degradation are known to have negative consequences for native biota, but the effects of small-scale disturbances such as selective logging are less well known. We compared three sites with different regimes of selective logging performed by Indigenous communities in the South American temperate rainforest, to assess effects on the density and habitat selection patterns of the Near Threatened endemic arboreal marsupial Dromiciops gliroides. We used structured interviews to identify patterns of wood extraction, which was 0.22-2.55 m3 per ha per year. In the less disturbed site only two tree species were logged, in the intermediately disturbed sites eight species were logged at low intensity, and in the most disturbed site seven species were logged intensively. The site with intermediate disturbance had the highest fleshy-fruited plant diversity and fruit biomass values as a result of the proliferation of shade-intolerant plants. This site also had the highest density of D. gliroides. These findings are consistent with Connell's intermediate disturbance hypothesis, suggesting that coexistence of people with nature is possible if wood extraction volumes are moderate, increasing plant diversity. Indigenous communities have sustainably used natural resources for centuries, but current rates of land-use change are becoming a significant threat to both them and their natural resources.