This chapter aims to further our understanding of the governance mechanisms that might best support a territorialised agroecological transition (TAET). The challenge of governance is to coordinate the actions of a multitude of actors and to integrate different dimensions of agroecology. This challenge is portrayed as important in the sustainable agri-food systems literature, which seeks a convergence of governance approaches pertaining to either a Socio-Ecological Systems (SES) or a Socio-Technical Systems (STS)-oriented conception. Starting from a representation of the territory that combines these two approaches, we emphasize the importance of reflexive governance for collectively constructing a shared space of values and knowledge between actors. Case studies of eco-innovative food and energy projects in rural areas of Gers and Aveyron in France illustrate various governance mechanisms. Even if there are high expectations pertaining to the territory as a place for articulating public, market, and civil society actors around a shared vision of sustainable agri-food systems, there is still a long way to go before local governance of the transition becomes a reality, including from a long-term perspective.