IntroductionDevolution reforms in Indonesia and Kenya have brought extensive changes to governance structures and mechanisms for financing and delivering healthcare. Community health approaches can contribute towards attaining many of devolution’s objectives, including community participation, responsiveness, accountability and improved equity. We set out to examine governance in two countries at different stages in the devolution journey: Indonesia at 15 years postdevolution and Kenya at 3 years.MethodsWe collected qualitative data across multiple levels of the health system in one district in Indonesia and ten counties in Kenya, through 80 interviews and six focus group discussions (FGD) in Indonesia and 269 interviews and 14 FGDs in Kenya. Qualitative data were digitally recorded, transcribed and coded before thematic framework analysis. Common themes between contexts were identified inductively and deductively, and similarities and differences critically analysed during an inter-country analysis workshop.ResultsFollowing devolution both Indonesia and Kenya experienced similar challenges ensuring good governance for health. Devolution reforms transformed power relationships, increasing responsibilities at subnational levels and introducing opportunities for citizen participation. In both contexts, the impact of these mechanisms has been undermined by insufficiently clear guidance; failure to address pre-existing negative contextual norms and practices varied decision-maker values, limited priority-setting capacity and limited genuine community accountability. As a consequence, priorities in both contexts are too often placed on curative rather than preventive health services.ConclusionWe recommend consideration of increased intersectoral actions that address social determinants of health, challenge negative norms and practices and place emphasis on community-based primary health services.