Small holders’ agriculture is currently facing new stakes due to State’s withdrawal from agricultural support and to higher market requests for producing agricultural products. Different coordination mechanisms can be observed inside the supply chains involving farmers, farmers’ organizations, and others stakeholders. They depend on the nature of the product, the characteristics of the stakeholders involved, the technical specifications related to the transactions, and the institutional environment. Relying on a comparative case study methodology, the paper analyzes the consequences of different coordination mechanisms on inclusion or exclusion of small farmers in the northern region of Costa Rica. Market coordination could be an efficient way to integrate farmers in supply chains in the case of low technical specifications and of existence of adequate selling mechanisms. Hybrid coordination is the main mechanism and facilitates the inclusion of small farmers, depending on the farmers’ organizations capacities to negotiate adequate rules. In some situations hybrid coordination with captive relationships could occur but leads to a more or less rapid exclusion process.