Uganda is the largest producer of organic commodities in Africa. While most of the literature associate the start of organic agriculture in Uganda with the first certified project, no accounts exist about non-certified organic agriculture before 1993. Both in Europe and in the USA, pioneers drove non-certified organic agriculture as a response to economic, ecological and social crises. Uganda suffered two decades of civil war ending in 1986 causing multiple crises. We explore how post-war conditions influenced the emergence of organic agriculture in Uganda. We conducted individual semi-structured interviews with 12 organic agriculture experts from Central and Southwestern Uganda. Interviews were held in English using interview guides informed by a transition theoretical perspective. Interviews were tape-recorded, transcribed and analyzed using deductive and inductive coding. Our analysis shows that the degraded environment, food insecurity and economic instability after the war created a sense of urgency for the rehabilitation of livelihoods. Pioneers, including civil society activists, farmers, entrepreneurs and researchers, responded by promoting low-cost, resource-conserving technologies and agronomic practices to smallholder farmers. Economic liberalization, decentralization and institutional vacuum eased pioneers’ activities, despite facing opponents from the government and research. Through experimental learning, demonstration farms and cooperation with the Catholic Church, public extension services, researchers and international development-oriented non-governmental organizations, pioneers reached out to farmers in Eastern, Central and Southwestern Uganda. As challenging as post-war crises may be, they offer opportunities for changing development trajectories. Therefore, reconstruction and rehabilitation efforts can accommodate sustainability concerns and allow the introduction of course-changing measures in any sector.