This paper presents learnings from community engagement and deliberation applied to ecosystem restoration and assisted adaptation in the Reef Restoration and Adaptation Program, a major research and development program identifying and testing novel management interventions for Australia’s Great Barrier Reef. Technical, social, and ecological complexities and uncertainties associated with the Program have a major bearing on both the need and character of community engagement and deliberation. Our research used qualitative analysis of documents, interviews, and group discussions to elicit transferable insights from a social research team embedded within the Program. Our findings demonstrate that adaptive and deliberative approaches anticipate and respond to complex and changing contexts by fostering open dialogue, building mutual trust, and integrating community feedback into decision-making. This practice actively recognizes the rights and interests of stakeholders and First Nation peoples, shaping stronger partnerships, supporting inclusive collaboration, and enabling flexible adjustments throughout research and development programs.