Dans les années 2000, des agriculteurs désireux de cultiver des blés correspondant à leurs besoins et soucieux d’affirmer leur autonomie vis-à-vis de l’industrie semencière, ont entrepris de relancer la sélection paysanne à la ferme. Des collaborations ont été tissées avec des généticiens de l’Inra, et se sont progressivement développées dans le cadre de projets financés. Or les financements de recherche impliquent une formalisation des partenariats, des engagements en termes de résultats académiques et une augmentation significative de la taille des projets. Dans ce nouveau contexte, comment préserver les valeurs d’émancipation paysanne et de justice cognitive sur lesquelles la collaboration paysans-chercheurs s’est originellement construite ? Cet article aborde la façon dont ce défi se pose concrètement aux acteurs de ces projets, et les précautions qu’ils mettent en œuvre pour y faire face. In the 2000s, a handful of farmers in France undertook to revive a practice fallen into disuse during agricultural modernization, i.e. on-farm plant breeding. Their motives were both to grow wheat varieties meeting their needs and to assert their independence towards the seed industry. Informal collaborations were woven with geneticists from the French institute for agronomic research (INRA), and developed further within the framework of funded projects. The foundations of a “decentralized participatory plant breeding” were then laid, both on a genetic rationale (breeding directly in the environments where the plants are to be grown) and on strong ethical principles (organizing non-hierarchical relations to let farmers question researchers’ assumptions). However, research funding involves a formalization of partnerships, commitments in terms of academic deliverables, and a significant increase in the size of projects. In this new context, how are the objectives of farmers’ empowerment and the values of cognitive justice on which the collaboration between farmers and researchers was originally built to be preserved? This article describes how this issue is actually tackled by the participants in these projects. We focus in particular on the debates raised by the creation of a database, and on the tensions it generates between centralization and decentralization. We also present the challenges raised by the dramatic increase in the number of participants, which risks to reproduce a division of tasks between researchers, farmers, and the people coordinating at a local level.