This open access book presents feedbacks from the TATA-BOX research project devoted to agroecological transition and its systemic, multi-scale and transdisciplinary issues. New conceptual and methodological frameworks and tools have to be developed to support local stakeholders into the design process of such a transition. The multidisciplinary and multi-organization research team led a four years action research process with two territories of France. The main project’s results are (1) key analysis of the specifics of agroecological transitions regarding diversity of agriculture models, management of uncertainties, polycentric governance, autonomies and the role of actor network, (2) presentation of an operational and original participatory process and associated boundary tools, (3) analysis of the main effects on research organization and on stakeholders’ development and application of the methodology, and (4) critical analysis of the main outcomes of TATA-BOX by external researchers.