Agricultural innovation is an essential component in the transition to more sustainable and resilient farming systems across the world. Innovations generally emerge from collective intelligence and action, but innovation systems are often poorly understood. This study explores the properties of innovation systems and their contribution to increased eco-efficiency in agriculture. Using aggregate data and econometric methods, the eco-efficiency of 79 countries was computed and a range of factors relating to research, extension, business and policy was examined. Despite data limitations, the analysis produced some interesting insights. For instance public research spending has a positive significant effect for emerging economies, while no statistically significant effect was found for foreign aid for research. However, foreign aid for extension is important in less developed economies. These and other results suggest the importance of context-specific interventions rather than a "one size fits all" approach. Overall, the analysis illustrated the potential of a macro-level diagnostic approach for assessing the role of innovation systems for sustainability in agriculture.