Cooperation plays a central role in the sustainability of agricultural value chains. This study analyzes cacao and dairy producer organizations in the Department of Caquetá, Colombia, with three objectives: to characterize their current organizational status, to understand legal representatives’ perceptions of the role of cooperation in strengthening their organizations, and to examine the structure of cooperation networks across different stages of the value chains. A qualitative approach was adopted, based on structured interviews, participatory network-mapping workshops, and secondary data analysis. The results show that cacao organizations exhibit higher levels of institutional consolidation than dairy organizations. Representatives’ perceptions indicate that in cacao, cooperation is primarily oriented toward administrative and strategic strengthening, whereas in dairy it is concentrated on production, budgeting, and marketing. Network analysis reveals a predominance of linking-type cooperation, characterized by vertical relationships with external actors, which enhances access to resources but also generates dependency. Overall, network structure and the prevailing types of cooperation influence organizational autonomy and collective performance in Amazonian contexts.