Transitioning toward more sustainable agricultural development paths requires extensive change and not simply marginal technical adjustments, as suggested by a strong conception of agroecology. To deal with transition, we believe that agroecology can be enriched by a deep analysis of sustainability transition frameworks and, conversely, that preexisting theories can be questioned in light of the specificities of agroecological transitions (AET). We first examine some of the main sustainability transition frameworks (resilience of social-ecological systems, institutional analysis and development of social-ecological systems, and socio-technical transition). We identify their ontologies to question their ability to be combined without deep adjustments. In a second step, we analyze how these frameworks have been used and questioned by researchers from the life sciences or social sciences in four AET studies. We find that each framework is relevant in its systemic and dynamic approach to change, but also that there are limits concerning the balance between the various dimensions. The scales and processes linked to AET must be taken into account, as well as the way to jointly consider ecological, socioeconomic, and technological aspects. Moreover, it is clear that problems in dealing with agency are common to these approaches, which influences the way to model change. More broadly, sustainability transition frameworks need to account better for ecological and technological materialities and processes, the importance of emergent organizations in singular situations, and learning processes and the diversity of knowledge dynamics. Doing so is challenging because it requires regrounding theories in empirical observations as well as questioning disciplinary frontiers and ontologies.