Rural communities have little say in their own future and in directing support to create the innovations to get there. Those with greatest need and the least voice – poor and smallholder farmers, women, youth – are precisely those most strategic to involve in order to reach the SDGs. These farmers and social groups are experimenters, producers of knowledge and researchers in their own right, hence they need to be empowered to drive the innovation processes. As key partners in co-research initiatives, development programmes and organizations that place their aspirations and capacities at the center, they can become dynamic, pro-active players in the pro-poor governance transformation of agricultural innovation systems. Approaches to improve governance include participatory research and foresight, institutionalizing the rights of rural women and recognizing farmers’ rights to genetic resources. Rights to access, use and ownership of open data by smallholder farmers are also crucial as data becomes the new frontier in agricultural development.