In this paper, the Global Value Chain approach is used to analyze the organic and fair-trade production of cotton in Mali and Burkina Faso. Two issues are raised: what are the producers’ advantages to produce organic cotton? Does it offer greater opportunities to create local added value? We compare the evolution of the respective profitability of the two global value chains in Mali and Burkina Faso. We point out the vulnerabilities related to the mode of governance of the organic and fair-trade GVC due among other factors to the weakness of yields, the narrowness of the market, the dependency on bailouts and the support of the NGOs and eventually to missing perspectives of local transformation.