The transition toward community-based tourism destination management requires policy implementation that balances cultural preservation, governance effectiveness, and economic sustainability. This study aims to analyze the implementation of an autonomous customary-based management policy following the transition from a government–community partnership model to an independently managed customary governance system. A qualitative approach with a case study design was employed. The research participants consisted of tourism destination managers, customary leaders, local government representatives, and community members involved in the management process. Data were collected through in-depth interviews, non-participant observations, and document analysis, and were analyzed using qualitative data analysis techniques involving data reduction, data display, and conclusion drawing. The findings indicate that the implementation of the autonomous management policy has been effective in terms of communication, resource availability, and implementers’ disposition, as reflected in improved management performance and substantial revenue generation. However, vulnerabilities remain within the bureaucratic structure due to overlapping authority among customary institutions. The study also reveals that the balance between the sacred and economic functions of the tourism destination has been maintained through the enforcement of customary regulations, spatial zoning based on local cultural principles, and the consistent implementation of religious rituals. These findings imply that an autonomous customary-based management model represents a viable alternative for tourism governance that is adaptive, sustainable, and capable of strengthening collaboration between customary communities and local government.