In the field of agroecology, on-farm experimentation often involves ‘co-design’ activities. This participatory openness exacerbates the challenges associated with the researcher’s stance and the use and goals of experimental approaches. To shed light on this situation and improve upon it, we conducted a reflective and comparative analysis of five agroecological projects involving co-design that were carried out by the co-authors. The aim was to identify and discuss how the use of co-design expanded and diversified the role of on-farm experimentation in scientific research. Three main themes arose from the analysis; each encompassed findings, lessons learned, and considerations to clarify the framework of collaborative on-farm experimentation. The first theme was related to the adaptable, contingent, and transdisciplinary nature of the examined projects. The projects followed a step-by-step design framework. The different phases of each project were completed using various methods and participation modalities, either sequentially or jointly. Farm fields and ponds were important places for social interactions and observations that fueled the ongoing processes of diagnosis, technique adaptation, and evaluation, and the development of shared assumptions and statements among academics and non-academics. The second theme addressed the different experimental approaches used and their relationships to scientific demonstration, depending on the objective of diagnosis and evaluation. We identified and conceptualized three approaches that were taken in the analyzed projects: practice-centered, ecosystem services-centered, and product-centered approaches. The third theme emphasized elements related to the transformative capacity of co-design activities with on-farm experimentation. It emphasized the influence of technical feasibility, expected gain, perceived risk, and the degree of systemic innovation required. Transformative capacity was associated with the conditions and development of the learning process, rather than the success of the innovative practices. This implies changes in farming practices that extend well beyond the project’s duration and are inadequately documented.