Food systems are changing through various socioeconomic and policy processes. For example, in France, following concerns over the effects of pesticides on ecosystems and health, the French government launched the “Ecophyto II+” plan in 2019 that aims for a 50% reduction in the use of pesticides by 2025. This top-down food system transformation is leading to conflicts between stakeholders over how to enact such a policy, and its implications for farmers and their practices. By adopting a transdisciplinary research approach, we explore conflicts linked to food system transformations in the context of three case studies in France. The case studies revolve around conflicts over pesticide use and reduction in three agricultural settings in Bourgogne Franche-Comté, namely (a) water management near Auxerre, (b) apiculture-agriculture relations in the Jura, and (c) viticulture-local resident relationships near Macon. We use four innovative transdisciplinary techniques to integrate inclusively the viewpoints of diverse stakeholders with the aim of generating actionable responses to transform food systems. First, the Community Voice Method (CVM) includes filmed semi-structured interviews and integrates a number of opportunities for participation and successive rounds of data analysis. Second, the interviewees were asked a “miracle question” that encouraged them to step back from conflicts and practices toward their ideal vision of agriculture and food systems. Third, the CVM resulted in the production of four films that relate the visions and perception of each case study interviewees in their own words and in their own setting. Finally, Transformation Labs (T-Labs) conveyed the main results of the CVM knowledge synthesis through the films produced and opened a dialogue toward the development of solutions. We review the four techniques, how they were implemented in the three case studies, and with which outcomes. Thus the aim of this paper is to offer reflections and lessons learnt from different transdisciplinary processes as a means of strengthening their application in other contexts. We argue that such methodologies, whilst resource-consuming, are essential to fully understand the complexity of food system transformations from the often-conflictual perspectives and competing knowledge claims of the multiple actors involved. In addition, we highlight the role of these techniques in building long-term trust between researchers and other stakeholders, and the benefits in terms of opening up dialogue and developing long-term solutions, as determined by the stakeholders themselves.