The development of sustainable agricultural and food systems is of significant importance considering the still-growing world population. For this, it is imperative to consider not only quantitative production issues, but also environmental issues such as water pollution, biodiversity loss, and land degradation as well as social and economic issues such as organization of supply chains and communication and coordination among stakeholders. However, the development of sustainable agricultural and food systems is so far almost exclusively proposed either at the scale of specific agricultural systems or for selected supply chains. Still strongly neglected is the development of sustainable systems at a territorial scale. We, therefore, present here the concept of agroecology territories. We define agroecology territories as places where a transition process toward sustainable agriculture and food systems is engaged. Three major domains must to be considered for the transition to take place: adaptation of agricultural practices; conservation of biodiversity and natural resources; and development of embedded food systems. Stakeholder group strategies, developed by those who actively engage in these three domains and are themselves actors in the transition, are integral to agroecology territories.