Top-down approaches to innovation development are still frequent or even dominant in many circles. Even after several decades, the shift away from such approaches is far from complete and has not happened without resistances. The first steps, up to introducing a fair degree of farmer participation in the research process, have been relatively painless because research-ers keep a fair degree of control over the research process. The subsequent steps leading to the developing of full-fledged partnerships have been much more difficult, because researchers are required to reassess thoroughly many conventional research methodologies and to scrutinize deeply held individual and institutional values and mechanisms about decision-making affecting the core of the research process. Understanding better such difficulties is the focus of this article. Drawing from a pool of 10 projects conducted by researchers working with farmers in a variety of contexts over the past decade, it provides insights and lessons about some major issues and out-lines specific challenges for the researchers involved in action-research in partnership.