Agroecology has been proposed as a strategy to improve food system sustainability, but has also been criticised for using land inefficiently. We compared five explorative storylines, developed in a stakeholder process, for future food systems in the EU to 2050. We modelled a range of biophysical (e.g., land use and food production), environmental (e.g., greenhouse gas emissions) and social indicators, and potential for regional food self-sufficiency, and investigated the economic policy needed to reach these futures by 2050. Two contrasting storylines for upscaling agroecological practices emerged. In one, agroecology was implemented to produce high-value products serving high-income consumers through trade but, despite 40 of agricultural area being under organic management, only two out of eight EU environmental policy targets were met. As diets followed current trends in this storyline, there were few improvements in environmental indicators compared with the current situation, despite large-scale implementation of agroecological farming practices. This suggests that large-scale implementation of agroecological practices without concurrent changes on the demand side could aggravate existing environmental pressures. However, our second agroecological storyline showed that if large-scale diffusion of agroecological farming practices were implemented alongside drastic dietary change and waste reductions, major improvements on environmental indicators could be achieved and all relevant EU policy targets met. An alternative storyline comprising sustainable intensification in combination with dietary change and waste reductions was efficient in meeting targets related to climate, biodiversity, ammonia emissions, and use of antibiotics, but did not meet targets for reductions in pesticide and fertiliser use. These results confirm the importance of dietary change for food system climate change mitigation. Economic modelling showed a need for drastic changes in consumer preferences towards more plant-based, agroecological and local foods, and for improvements in technology, for these storylines to be realised, as very high taxes and tariffs would otherwise be needed.