INTRODUCTION: In the backdrop of the Sustainable Development Goals (SDGs), the state of Kerala, India, revamped its existing primary health centres (PHCs) into people-friendly family health centres (FHCs) in order to provide comprehensive primary care as part of a mission-based ( ‘Aardram’ ) initiative. It was envisioned that the mission’s implementation and operation would make use of decentralised governance. The present study explored how the decentralised governance influenced reorganisation of primary care. METHODS: The study adopted an exploratory approach using qualitative methods: key informant interviews ( n = 8), in-depth interviews ( n = 20) and document reviews. Thematic analysis was done following deductive coding and the themes that emerged were organised under a schema. RESULTS: The results could be summarised under five overarching themes. Strong political commitment, combined with bureaucratic competence, facilitated implementation and functioning of ‘Aardram’ primary care. The insights developed through multi-sectoral training helped local governments (LGs) get involve and engage with the health system as a team in order to plan and implement interventions. The decentralised governance structures enabled re-engineering of PHCs by mobilisation of financial resources, provision of human resources, infrastructure modification, and enhanced community participation at various levels. Non-uniformity of commitment, sub-optimal engagement of urban LGs and issues of sustainability and monitoring were the shortcomings observed. CONCLUSION: Decentralised governance played a positive role in the re-engineering of PHCs, which was utilised as a platform to demonstrate best practices in health governance through a participatory approach. The importance of empowering LGs through capacity building to address challenges in achieving primary care SDGs is highlighted in this study.