Third-party certification (TPC) is becoming an integral component of the global agrifood system. However, little is known about its functions, structures and practices. In this article we examine the emergence of TPC as a governance mechanism, its organisational structure, and its practices. Distinguishing between two forms of ‘independence’– organisational and operational – we argue that TPC exhibits organisational, but not operational independence. Thus, in contrast to the view of TPC as an objective governance mechanism, we argue that TPC is embedded in social, political and economic networks. This finding, we argue, raises questions as to how TPC is structured and operates, who gets to decide the ways it is structured and operates, and the ways that TPC might differentially impact on actors in the food and agricultural sector.