Agroecological principles and transitions can create tensions between initiatives rooted in social movements and institutionalisation processes. This pulls researchers between two potentially conflicting tasks: (i) advising policymakers and (ii) supporting farmers and stakeholders in their endogenous trajectories. This paper addresses this tension by focusing on the role of academics in transdisciplinary long-term collaborations. The study reviews a two-day transdisciplinary workshop organised by the “Lands and Soils'' knowledge community (CoSav Terresol) hosted by the French National Research Institute for Sustainable Development (IRD). Forty participants, including researchers, NGOs, farmers and policymakers’ representatives, engaged in reflexive activities to explore various agroecology narratives and the issue of researchers’ postures in agroecological transitions. The findings highlight the need for transversal skills and facilitators to support researchers in dialoguing with different stakeholders. This includes the importance of deconstructing narratives and considering the ethical implications of long-term partnerships in producing agroecological knowledge. In this way, engaging in a transdisciplinary dialogue that recognises farmers' knowledge and considers farmers as research actors and partners is crucial.