Chapter 3 sets out the functioning of the EAEU in terms of its institutional structure and decision-making. It is particularly focused on the Eurasian Economic Commission as the main regulatory body due to its alleged supranational character. This chapter challenges the idea of supranationality by uncovering the predominantly intergovernmental mode of operation not only of the EAEU as such, but also of the Commission, which has implications for legal order autonomy. Another focus of the chapter is the Court and its structure as the major institution relevant for legal order autonomy. The chapter analyses the history of its establishment and the rules regarding its formation raising the issue of independence of the judges and the institution as relevant for the Court’s ability to play a role in the formation of the autonomous legal order.