Agroecological transition requires that innovative and diversified cropping systems be developed. Conducting system experiments is an approach well-suited to the analysis of performance of cropping systems when subjected to soil, weather and biotic stresses. Conducting system experiments nevertheless gives rise to methodological challenges. Using the Syppre network of experiments, consisting of five sites in France, we present an original case study that provides valuable methodological and agronomic lessons on system experiments. The innovative cropping systems tested there are based on crop diversification (including oilseeds and protein crops), as well as flexible tillage, technical innovations and optimized crop management. From a methodological standpoint, we show that (i) mixed models are adapted to a range of experimental questions and constraints; (ii) multifactorial analysis enables the characterization of relationships between performance indicators; (iii) a multisite experimental network is an efficient approach not only for answering agronomic questions, but also for addressing methodological issues. From an agronomic standpoint, we showed that reconciling multiple indicators of performance is still challenging. Overall, innovative and diversified systems improved the performance of input utilization and environmental impacts, but with lower productivity and profitability. Introducing legume crops is a promising strategy because this contributes significantly to reductions in mineral N fertilizer use, energy consumption and greenhouse gas emissions, without major trade-offs against other performance indicators. Finally, we showed that the nature of the production situation had a major influence on the performance profile. This led us to be cautious in making overall analyses especially with regard to general conclusions.