The industrialization of farming has significantly threatened cultivated biodiversity. Participatory breeding endeavours to overcome this issue by enabling farmers to select a wide range of crop varieties in different conditions, and to foster genetic mixing through seed exchanges, crosses or mixtures. This necessitates the design of new forms of coordination and organization for the farmers and partners involved. This article reports on an ongoing initiative, aiming to facilitate the participatory design of such forms of coordination and organization. It first outlines the method used (Knowledge–Concept–Proposals or KCP), and how it has been tailored to this highly decentralized context involving politically engaged actors on a quest for autonomy. It then presents the exploratory results of the first two workshops: these include group consolidation, the sharing of heterogeneous knowledge, the generation of innovative ideas, and the elaboration of preliminary projects. Finally, this empirical case is compared with other initiatives supporting the participatory design of natural resource management strategies and tools. Its key original dimensions and benefits are that the workshop protocol is replicable, the data produced can be easily exploited, and it allows for testing hypotheses in the field of design science.