In recent years, the transition to sustainability at a food systems’ scale has drawn major attention both from the scientific and political arenas. Agroecology has become central to such discussions, while impressive efforts have been made to conceptualize the agroecology scaling process. It has thus become necessary to apply the concept of agroecology transitions to the scale of food systems and in different “real-world” contexts. Scaling local agroecology experiences of production, distribution, and consumption, which are often disconnected and/or disorganized, also reveals emergent research gaps. A critical review was performed in order to establish a transdisciplinary dialogue between both political agroecology and the literature on sustainable food systems. The objective was to build insights into how to advance towards Agroecology-based Local Agri-food Systems (ALAS). Our review unveils emergent questions such as: how to overcome the metabolic rift related to segregated activities along the food chain, how to feed cities sustainably, and how they should relate to the surrounding territories, which social subjects should drive such transitions, and which governance arrangements would be needed. The paper argues in favor of the re-construction of food metabolisms, territorial flows, plural subjects and (bottom-up) governance assemblages, placing life at the center of the food system and going beyond the rural–urban divide.