Sustainable food supply chains are complex systems involving several stakeholders, processes, flow of goods/materials and information. The value generated in combination with the contradictory agendas among actors makes any groundwork for future research a challenging endeavor. Hence, an end-to-end mapping of the food supply chain under examination is a vital prerequisite for the design of a comprehensive research framework. This study exemplified such a mapping approach in the Greek sustainable tomato supply chain, providing significant insights for an impactful research agenda. Data were obtained from secondary sectoral sources and open interviews with key players across the supply chain—covering all its main stages, i.e., production, packaging, storing, transportation, wholesaling, and retailing. The findings are summarized in three supply chain maps that illustrate the areas concerning sustainability, value chain and stakeholders. These maps synthesize a bigger picture of the supply chain that reveals the complicated interactions among its actors, the hidden bottlenecks in the flow of information and the areas that need deeper exploration. Its fundamental implication is the design of a targeted research framework, underlying the main priorities of the Greek tomato supply chain and eventually the Greek agri-food sector.