Several agroecology scholars have called for transdisciplinary, participatory action-research to transform unjust and unsustainable food systems. We reflect on the methodological, theoretical and practical challenges that such an approach raises, based on the case study of an interdisciplinary engaged research project on farmer autonomy and agroecology led in Southwest France. The project’s focus on farmer autonomy aimed at re-politicising agroecology by paying attention to farmers' dependency relationships within dominant political, cognitive and economic structures and at engaging with a large diversity of farmers. Despite strong links between agroecology and autonomy, most studies on farmer autonomy have paid little attention to ecological processes. Based on qualitative primary data, we explore the relevance and limitations of farmer autonomy as a bridging concept between social and ecological science, as a boundary object among non-academic partners and as a rallying flagship for action. We therefore hope to contribute to several under-explored areas by political ecology scholars: better considering ecology while adopting a critical epistemological stance and conducting engaged research on farming systems in the Global north.