The purpose of this article is to study the transplantation of complex agro‐industrial systems. The main focus is the analysis of the biodiesel system in Brazil using the Agro‐Chain System approach (AGS). The AGS analysis considers the institutional and organizational environments and verifies how a governance structure evolves as the institutional environment changes. The methodology used is a case study of the biodiesel chain system in the State of Minas Gerais – Brazil. This local system developed as a result of governmental incentives. The present study’s contribution is that it identifies the main obstacles to implementing agro chains and networks involving regions and actors that do not have previous history of productive organizations.