Why and how organic agriculture has been developing in Africa is under-studied, especially from a political stance. We explore two contrasting empirical case studies of national organic trajectories: Uganda and Benin. In both countries, organic agriculture emerged in the 1980s around food security stakes and spread in the 1990s through certified export value chains, with a faster development in Uganda than in Benin. From a theoretical perspective, this paper proposes an original analytical grid to study national trajectories of institutionalization of organic farming in Africa, based on three main variables: the policy regime in place in the country (including socioeconomic and agrifood dimensions); the relative interest of public and private foreign actors in organic agriculture; and the strength of the national organic agriculture movement. Our results show that the degree of institutionalization of the Green Revolution paradigm in the country is of capital importance for explaining developments in organic farming, particularly its materialization through the increasing use of synthetic inputs: institutionalizing organic farming means deinstitutionalizing agrochemicals. We also show that the high level of extraversion of organic agriculture development in Africa through its focus on certified export value chains raises long-term questions of farmers' empowerment and of local consumers/citizens' access to local organic food. Finally, national organic agriculture movements can play a crucial role by politicizing certain issues in national public debate, such as pesticides' impacts on human and environmental health, and by advising governments in organic policy framing and implementation. Applying the proposed socio-political analytical grid to new national or regional African case studies will help to further enrich the empirical knowledge on organic food and farming in Africa.