Crop diversification represents a key lever to support the development of sustainable agri-food systems. Knowledge on trade-offs and carry over effects from different crop diversification strategies is essential to inform agricultural stakeholders of potential costs and benefits. This knowledge is limited by existing data and performance measures predominantly focused on single crops, rather than complete rotations. Moreover, sustainability performance indicators are often used for assessment purposes, rather than supporting stakeholder learning and actions. A new set of 32 indicators was developed to address these needs, and used to evaluate the environmental, economic and social sustainability of the diversified agricultural systems highlighted in the case studies, which are often characterized by data availability constraints. This approach was tested in France, Germany and Italy to determine a critical ex-post diagnosis of the existing systems, and for the assessment of ex-ante innovative scenarios. The results will be used to support these case studies in the identification and design of more sustainable agricultural systems. Although the framework is based on feasible and proxy indicators, the assessment outcomes have allowed local actors to reflect on the effects generated by the implemented crop diversification strategies. Key issues include trade-offs occurring between optimizing economic and environmental performance.