This article examines the contentious issue of the coexistence of cheese made from raw milk and cheese made from pasteurised milk in areas of protected designation of origin (PDOs). The French PDO system is held to be the benchmark of the international system of geographical indications (GIs). Drawing on the multi-level perspective framework of socio-technical transitions, we conceptualise PDO cheeses as a “niche” nested within a dominant regime that promotes pasteurisation as the standard technology to control pathogens in milk. Careful examination of statistical data and the specifications for PDO cheeses shows that raw milk is experiencing an upturn in domestic production, which we relate to the reinforcement of the regulatory frameworks governing protection of GIs. We investigate more fully the steady increase in raw milk use by studying two contrasting cases of PDO cheeses (Saint-Nectaire and Ossau-Iraty), in which the confrontation between technologies is internalised. Analysis of local innovation pathways highlights a series of key decisions that strengthen the position of raw milk from the farm to the marketplace, namely grass-feeding, limiting herd productivity, technology-specific identification marks, and redistribution of decision-making power among stakeholders. Regulatory mechanisms that counterbalance the pressures of the regime by strategic management of the “terroir” niche are identified and discussed. We argue that shifting the focus from niche/regime interaction towards the internal dynamics of niches sheds light on the conditions of a coexistence of apparently antagonistic models of production in agri-food networks.