Involving users in the development of innovations has become not only legitimate, but necessary, especially when users face strong constraints. The Unai project in the Brazilian Cerrados is using such an approach for accompanying small holders of the Agrarian Reform sector in their struggle towards sustainable agriculture. Several stakeholders are involved, including research, education, local development institutions and farmers. Direct-seeding systems (DSS), improved livestock feeding and milk marketing, and also capacity-building of farmers and their organizations are among the key innovations being tackled. The paper highlights results obtained with focus groups in developing milk marketing and directseeding, in their technical, organizational and training / learning dimensions. The Unai project also facilitated the emergence of a new cooperative extension service comprised of young farm advisers originating from the Agrarian reform sector households. Work is also under way to help farmers and their organizations play a more active role in the emergence of sound agricultural policy instruments at the level of the whole Unai region. More generally, the Unai project strives to give a concrete meaning to key concepts such as responsabilizing farmers, formalizing the relationships among stakeholders, negociating rules for collective action, adjusting dynamically the roles and functions of the various partners, and favoring mutual learning. In doing so, it aims to enable all stakeholders, and especially the weaker ones, to gradually become true co-designers of innovations. Installing effective mediation and catalyzer functions, developing effective strategies for coping with conflicts, risk and unexpected occurences, reasoning the dynamics of interventions over time and at multiple scales, and finally creating adequate space for mutual learnings are part of the continuing challenges the Unai project faces. This experience illustrates the interest and challenges of approaches aimed at rejuvenating the thinking and the practice of how research may accompany innovation processes. Implementing the corresponding changes require time and continuity of efforts. It also requires active, imaginative support by the institutions hosting the corresponding work, with the eventual aim of achieving an effective integration of scientific and institutional approaches on one hand, and of agronomic, ecological and social sciences on the other hand.