Community-based conservation is advocated as an idea that long-term conservation success requires engaging with, providing benefits for, and establishing institutions representing local communities. However, community-based conservation’s efficacy and impact in sustainable resource management varies depending on national natural resource policies and implications for local institutional arrangements. This paper analyses the significance of natural resource management policies and institutional design on the management of common pool resources (CPRs), by comparing Namibian conservancies and community forests. To meet this aim, we reviewed key national policies pertinent to natural resource governance and conducted 28 semi-structured interviews between 2012 and 2013. Key informants included conservancy and community forest staff and committee members, village headmen, NGO coordinators, regional foresters, wildlife officials (wardens), and senior government officials in the Ministry of Environment and Tourism and the Ministry of Agriculture, Water and Forestry. We explored the following questions: how do national natural resource management policies affect the operations of local common pool resource institutions? and how do external factors affect local institutions and community participation in CPRs decision-making? Our results show that a diversity of national policies significantly influenced local institutional arrangements. Formation of conservancies and community forests by communities is not only directly linked with state policies designed to increase wildlife numbers and promote forest growth or improve condition, but also formulated primarily for benefits from and control over natural resources. The often-assumed direct relationship between national policies and local institutional arrangements does not always hold in practice, resulting in institutional mismatch. We aim to advance theoretical and applied discourse on common pool resource governance in social-ecological systems, with implications for sustainable land management policies in Namibia and other landscapes across sub-Saharan Africa.