The application of participatory methods for codesigning sustainable land uses in research and development (R&D) projects for the agroecological transition are receiving increasing attention. However, there has been limited research critically assessing participatory methods employed in a codesign process. We therefore analyze the participatory methods applied for codesigning alternative land uses in the Sustainable Amazonian Landscape (SAL) project in the Caquetá department, Colombia. We conducted our analysis by situating the codesign process in a participation continuum and a codesign typology. We found that a gradient of participation level in the R&D project is beneficial for managing a codesign process. Thus, codesigning can be shaped during the project to respond to specific needs, and farmer participation levels change during the project. We found that codesigning is a process that only partially relies on participatory methods epistemologies. Instead, it reflects a tension between the continuity of a codesign project in a given territory, the sustained involvement of local partners, and external conditions such as socioeconomic and institutional stability. These are essential points to consider for co-designing the agroecological transition, as we suggest that these project-based research conditions might hinder critical principles of the codesign process.