Transition towards ecological intensification in agriculture is a knowledge intensive process that should not be perceived as the promotion of old traditional practices. The science supporting such an option is relatively young and its analytical framework has not been tested over many years. It is therefore important to identify and address what we poorly know, that is understanding bio-ecological mechanisms at work in agrosystems, using agro-biodiversity as leverage for intensification, exploring the multiple and complex links between the technical dimension of practices and socio-economic and political changes. This means revisiting the notion of performance in agriculture. This also leads to orchestrating research partnerships, at local and global levels, and implement multistakeholders' original learning approaches that embed scientific knowledge into local innovation systems. After describing the specificity of knowledge gaps, this contribution identifies the main knowledge gaps and explores new research approaches, arrangements and roles.