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With the rise in participative approaches and the attempts to include environmental issues in agricultural practices, knowledge production in the field of agriculture appears to lie at a crossroads between methodological challenges and fundamental issues about the scientific research profession itself. How should researchers gain access to farmers’ knowledge, and for what purpose ? How do farmer and researcher sets of knowledge interact ? What should researchers do when knowledge becomes a source of tension in collaborations with stakeholders ? This article contributes reflections that emerged during the design and facilitation of a training program organized by Inra and Cirad in 2016. It aimed to develop researchers’ reflexivity when analyzing and acting in these knowledge-intensive situations. We analyze the stages of the design process and the interdisciplinary exchanges that the latter required within the organization team, as well as the educational framework chosen and its impacts during the training stage.