CIRAD has been engaged over the past few decades in supporting actors of agri-chains in countries of the South in their processes of change and innovation. Research in partnership has become a preferred modality of research and development but its benefits and limitations are not always well understood. Since agricultural innovation is not necessarily linked to the direct application of research results, new approaches centred on innovation processes and systems have been proposed in order to rethink the contributions of researchers and modalities of intervention. This chapter presents the theoretical foundations of the links between innovation processes, organizations of agri-chains, and capacity building. A systemic approach to innovation and the theory of transition are key elements in highlighting the contributions of research. The implementation of methods to monitor and evaluate the impact of research on innovation and agricultural development is also a major challenge for improving the performance of research and development practices within the agri-chains.