Researchers worldwide are expected to design and develop agroecological systems to address major challenges such as increasing biotic pressure and climate change. But to design effective innovations, researchers should integrate new cropping techniques into wider agricultural systems such as cropping systems, innovative farms, alternative food systems, or multifunctional landscapes. This integration requires a long process of exploration in which the object under design can transform and shift to a different organisational scale. In this article, we wish to introduce a new analytical framework highlighting the systemic mechanisms involved in the scale transformations of design objects along agroecological design processes. We conceptualise an agroecological design process as a non-linear unpredictable process in which four components—a science consortium, non-scientific actors in the field, a problem situation and a design object—interact, and co-evolve through time. The scale transformations of the design objects and their drivers are the results of interactions and knowledge flows between these four components. This analytical framework was tested and further elaborated through ex-post analysis of design processes in three contrasting case studies in the context of tropical horticulture. Data were collected through literature review, interviews, and focus group discussions with the researchers involved in the three design processes. Future design methods should take full account of the lengthy, non-linear, and transformational nature of agroecological design processes and the coexistence of different types of knowledge—holistic vs. reductionist, ecosystem focused vs. human-system focused—which can interconnect and nourish each other.