Agricultural research is expected to foster agro-ecological transitions. For that purpose, methodologies of participative integrated assessment of new farming and cropping systems are requested. However, the territory level and the stakeholders’ participation are often not sufficiently embraced. Based on the companion modeling approach, a group of researchers from different disciplines experimented an approach where researchers and stakeholders collaborated intensively all along the process of design and use of the model. The researchers selected a small rural area where agriculture plays a major role (Valensole plateau, south of France) and where they had not carried out any investigation before. In such conditions, we argue that the interactions between researchers and stakeholders involved in the co-design from scratch of a simulation model stimulate a collective reflection about the sustainability of current and alternative farming systems. This article describes the different phases of the process from stakeholders’ enrolment until the final discussion of the results provided by the model. It underlines the conditions that favored the emergence of consensus and the production of a new set of knowledge. It emphasizes how the discordances between data and disagreements between stakeholders were used to stimulate collective debates and underlines the role played by the model. Finally, the article discusses the drawbacks that the approach did not overcome.