The need to reconnect agriculture, environment, food, and health when addressing agrifood system transitions is widely acknowledged. However, most analytical frameworks, especially in the expanding literature about “system approaches”, rely on impact-based approaches and, thus, tend to overlook ecological processes as well as social ones. This article aims at demonstrating that a territorial approach to agrifood system transitions is more appropriate to tackle the reconnection between agriculture, food, environment, and health than the larger scales (global or national food systems) or the smaller ones (such as those of alternative food systems) usually addressed in the literature. Co-elaborated by a sociologist, an ecologist, and a nutritionist, this article is based on a focused analysis of the literature that has addressed agrifood system transitions in the food and health sciences and in the social sciences and on the reflexive analysis of two past projects dealing with such transitions. It shows that a territorial approach allows including in the analysis the diverse agrifood systems’ components as well the ecological and social processes that may create functionalities for improving agrifood systems’ sustainability. This territorial approach is based on systemic and processual thinking and on a transdisciplinary perspective combining an objectification stance and a pragmatist constructivist one. It should allow actors and researchers to build a shared understanding of the transition processes within their shared territorial agrifood system, despite possibly different and diverging views.