Innovation is ultimately linked to the human desire to think about new and better things and to try them out in practice. In this article, we suggest farmer participatory research as an approach to foster community-led innovation in smallholder agriculture in western Uganda. Farmer participatory research is a process of designing and implementing on-farm trials to test and further improve agricultural technologies and agronomic practices. For smallholder farmers who lack access to formal agricultural research and support services, farmer participatory research supports community-led innovation aimed at improving ecological sustainability agriculture.