Industrial agriculture and its requirement for standardized approaches is driving the world towards a global food system, shrinking the role of farmers and shifting decision-making power. On the contrary, a holistic perspective towards a new food-system design could meet the needs of a larger share of stakeholders. Long-term experiments are crucial in this transition, being the hub of knowledge and the workshop of ‘participation in’ and ‘appropriation of’ the research in agriculture over a long term. We present a methodology applied during the creation of a small network of organic farmers in Italy and detail the steps of the co-innovation process implemented. After a context analysis of the area to define the type of research and degree of participation, three steps were performed: (1) Identification of stakeholders; (2) dialogic identification of common activities; and (3) validation and feedback from participants. In the first participatory step, five organic farms were engaged for the second and third steps. We organized meetings to discuss future plans, facilitating the interaction process between farmers and researchers. These activities led to: (i) the definition of a research protocol based on farmers’ research needs for a new long-term experiment; (ii) committing farmers to take an active role in the research; and (iii) hosting experimental satellite trials in their own farms.