Agricultural expansions and unsustainable resource extraction increasingly threaten biodiversity worldwide. Thus, knowledge on landscape management opportunities that contribute to biodiversity conservation and provide the necessary natural resources is urgently needed. Community-based natural resource management can be one solution to achieve sustainable resource provisioning and biodiversity conservation. However, evidence on the effectiveness of the management transfers to local communities for biodiversity conservation is scarce. We use a case study from south-western Madagascar to discuss the integration of community-managed forests, including forests protected by local taboos, into measures for biodiversity conservation. In particular, we compared reptile community composition and species diversity between differently managed forest sectors (used and less-used) in two community forests. We hypothesized that forest use affects biodiversity depending on the people’s acceptance of management regulations. Our results show that reptile community composition was affected by forest management if the less used forest part was protected by traditional taboos. If the people did not respect regulations for resource extraction, habitat protection failed which led to a homogenization of reptile community composition across different forest parts. This highlights that the type of forest management and use and its acceptance in the rural communities determines the contribution of community forests to biodiversity conservation.