Successful transitions to agroecology require shared understanding of the sustainability implications of transitions for food systems. To gain such understanding, a transdisciplinary approach is increasingly called for by funders, end users of research and scientists. Transdisciplinary processes were used in the UNISECO project to develop strategic pathways that enable transitions to agroecology in case studies across Europe. These strategic pathways were combined with scenarios of EU food systems in 2050, in which combinations of agroecological farming and food consumption practices were assessed. These were then reviewed considering selected UN Sustainable Development Goals (SDGs) as a reference for discussing the sustainability implications of transitions to agroecology. Sustainability implications were identified for several SDGs including Zero Hunger (SDG 2), Quality Education (SDG 4), Responsible Consumption and Production (SDG 12), Climate Action (SDG 13) and Life on Land (SDG 15). Key factors contributing to the sustainability of transitions to agroecology are: i) mature social capital and improved farmer knowledge of the benefits of agroecological practices; ii) strengthened collaborative actions and collective institutions to increase negotiating power within the value-chain; and, iii) changes in consumer behaviour and diets. These factors highlight the need for a food system perspective in transitions to agroecology and supporting policies. This in turn highlights the meaningful role of transdisciplinary research in strengthening the sustainability of European food systems.