Rural tourism is prominent in promoting sustainable use of resources and is implemented in Indonesia through a tourism village program. Present study explores resource management strategies in two Balinese villages, providing new and comparative insights into the underrepresented high customary setting. Data were collected through multiple qualitative methods and analysed using thematic analysis. Findings support the need for customary and community involvement in retaining local control over resources, collectively enabling the effective use of infrastructure and workforce. These allow co-creative experience-making and storytelling to facilitate resource conservation. Two management challenges and a management outcome of a spiritual belief in Tri Hita Karana (three harmonious relationships) were identified. The findings revealed the challenges, outcomes and strategic use of tourism resources for the improvement of the tourism village program. Our contributions concern the importance of harmony between spirituality, people and nature, customary involvement and conservationist resource reinterpretation in rural tourism resource management.