Many questions and debates are being undertaken in the literature about the “context-specific transition pathways of agroecological transformations and their related conceptual, political, institutional, social, and other challenges and opportunities. Pilot projects for Agricultural Research for Development (AR4D) are key areas where these questions and related assumptions can be tested, piloted, and reported for better lessons and future conceptualization. In this paper, we present the experience of the One CGIAR Initiative on Agroecology transformation for food, land and water systems, which adopted a transdisciplinary, participatory, and action-oriented approach aimed at enhancing food system resilience, equity, and sustainability. Even though the theory of change (ToC) of this initiative was quite clear and robust, its application on the ground, in seven countries, faced a strong challenge of contextualization, which then guided further adjustments of this ToC to better match local expectations thus leading to locally co-identified (co-designed) transition pathways which are the most relevant to local socioecological systems as well as to stakeholders' preferences and objectives. The paper presents some progress of the initiative implementation from Tunisia case studies thus highlighting a realistic approach (suite of activities), refined with national partners and local communities, for participatory co-design of “Agroecological Transition Pathways” at the living landscape (ALL) and food system levels. The identified (realistic) approach is composed of 10 key steps staring from 1) clearly defining the geographical and conceptual frontiers and intersections between living labs, innovation systems, production system, value chains, socioecological systems, etc. which will then support the clarification and identification of action areas and levels of operation of the ongoing program, 2) Stakeholders' mapping at different levels with identification of synergies and