Though GI systems can be significant institutional tools to link producers, territories, and agri-food products, their outcomes are conditioned by the way in which quality and code of practices are socially constructed. In some cases, powerful stakeholders have attempted to co-opt GIs and insert industrial logics and modern technology, which undermines the objectives of GI systems to protect producers who adopt traditional and local production methods. Employing the case of Hatcho Miso, this chapter aims to analyze Japan’s GI system and its first nation-wide controversy over the registration of a GI. This study is based on a field survey with semi-structured and open-ended interviews conducted from 2015 to 2024 among stakeholders as well as on literature review. It concluded that the case of Hatcho Miso shows that the alienation of traditional manufacturers is arising in the Japanese GI system, and that private territorial labeling such as Honbano Honmono has more potential to differentiate the quality and authenticity of agri-food products than the existing GI system in Japan.