Background Engaging relevant stakeholders throughout the research cycle is increasingly recognised as critical to conducting quality health systems research. There are few descriptions and analyses of stakeholder engagement in practice for embedded health systems research especially those that must navigate multi-level decentralised health systems. We describe and reflect on the stakeholder engagement activities of an international multi-disciplinary programme of research focused on newborn care in hospitals in Kenya. Methodology Our experienced project stakeholder engagement group coordinated engagement activities across multiple stakeholders with differing interests in the research. We conducted a stakeholder mapping and analysis using an engagement matrix to include national and county-level policymakers, professional communities, associations and regulators, health managers, frontline healthcare workers, patients, families and patient representative groups. Our engagement group maintained a log of engagement activities and had regular programme feedback meetings and discussions. As part of our analysis of stakeholder engagement, we drew on project documents and meeting minutes, and on a conceptual framework which distinguishes between the moral, strategic and practicaldimensions of stakeholder engagement. Results Stakeholder engagement was essential but complex in practice. Although we had significant prior engagement experience and relationships at the hospitals and the counties, introducing new staff into NBUs triggered complexities that required careful consultation along the bureaucracies at the counties. Despite the counties having similar hierarchical architectures, engagement processes varied and achieved different outcomes across counties. There were also multiple officeholder transitions over the research period, occasioned by factors in our external environment, often necessitating engaging afresh. Conclusion Even with a carefully developed stakeholder engagement plan, an experienced team, and a landscape backed by long-term embeddedness, health research stakeholder engagement can unfold in unexpected ways and requires continuous effort, resources, and adaptability. Meeting the moral, strategic, and practical potential of engagement requires flexibility, responsiveness, and commitment, including adequate resources.
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