Agroecology is a new paradigm whose aim is to redesign farming systems. The implementation of its principles engages farmers in a radical transformation of their practices, their way of reasoning and their participation in local knowledge production and innovation processes. Acknowledgement of this transformation now frequently leads researchers to invite farmers and other stakeholders to participate in research projects on the design of innovative farming systems. However, the objective of their involvement and the role farmers play in such projects is rarely made explicit and can range from simple knowledge providers to co-designers. Here we review the role of farmers and other stakeholders in such participatory research projects, and its impact on their learning and engagement in the local transformation of farming systems. Using a framework based on design theories, we analyzed thirty-nine papers on the design of innovative farming systems in which farmers and other stakeholders were involved. We identified five main co-design approaches to the design of agroecological farming systems: "De-novo design", "Case-study design", "Niche innovation design", "Co-innovation", and "Activity centered design". Despite this diversity, if researchers aim to promote the development of agroecology, there a still need to better link researcher-oriented approaches and support-oriented approaches, to design local set-ups that will help farmers and other stakeholders in the long term process of redesigning farming systems. In terms of design methodologies, this means sharing project leadership with farmers and organizing co-design locally to better bridge the gap between thinking and doing. This means better accounting for the singularities of farmers' situations and of the local activity system to be transformed. This paper should help researchers choose their participatory methodologies better with respect to both to their transformational and scientific goals, when organizing participatory projects to support the development of agroecological farming systems.