Organic farming and fair trade certified chains have emerged in West-Africa since the 1990s in answer to new alternative markets in developed countries. These chains, involving actors from North and South, are seen as an opportunity to sustainably valorise the small peasants agriculture in Africa and include the smallholders in global markets. Certification and labelling systems accompany these chains in developed countries. The aim of this article is to analyze the challenges for smallholders of this new North- South trade regime established by certificates and labels. This article uses the theory of Global Value Chains as theoretical framework. The empirical framework consists of four cases (organic sesame; organic- fair sesame; fair cotton and organicfair cotton) in Mali and in Belgium and France. It focuses on data that are gathered during our inquiry based on a questionnaire with the chains stakeholders in the south and in the north. The chains upstream inquiry was conducted in Mali with individuals producers, producers organizations, exporters; and the downstream inquiry was conducted in Belgium and France with European importers, distributors and certifications bodies. The results show that the new North- South regime established by organic and fair certificates and labels has a potential impact on the negotiation power and value distribution between chain participants. Lack of adequate local institutions in Southern countries, and increasing complexity of the “cahiers de charges” imposed by the North however may cause exclusion of many smallholders in these new North-South trade networks.