A variety of sustainability standards have emerged from social movements that stake claims on different niches in the market for sustainable food and agriculture products. We argue that we are beginning to see a transition towards a regime of ‘certified sustainability’. This regime is characterized by the use of standards to govern agri-food systems and a second layer of standards to govern the standards. In this chapter we ask how this regime is constructed and how standards are used to govern the transition to sustainability. Drawing upon a case study of the International Social and Environmental Accreditation and Labelling (ISEAL) Alliance’s assurance code development process, we highlight the framing practices that characterize the shape of a multi-layered governance of ‘governing by standards’. We discuss how the framing of certified sustainability opens up new issues like the relationship between credibility and legitimacy, the embodiment of skills in auditors, or the call for evidence-based systems in order to tame risk. These activities have implications for how change is governed in socio-technical and innovation systems.