Background: Geographical indications (GIs) are collective intellectual property rights that protect food and other products uniquely linked to the production area, local geophysical conditions, and traditions, namely, with the terroir. Thus, GIs can contribute to the transmission and retention of culinary heritages and historical production practices. Methods: Based on an analysis of application documents, we compare the historical linkages of all the Japanese and Austrian GI products. Although more than half of the Japanese applications refer to historical roots in the 20th century, the median of the Austrian GI linkages is in the 17th century. To closely examine these GI linkages, and to better understand their relevance to current cultivation practices, we compared three Japanese cases with roots of diverging depth to the first Austrian GI regarding motivations, geographical and historical linkages, and current cultivation practices and governance. Results: The comparison found that all four products refer to the historical roots of the product name, the product varieties, or cultivation techniques. However, deeper roots did not automatically translate into higher priorities of protecting these historical linkages. The four in-depth case studies found that historic provenance and traditional production methods, although prominently highlighted in the official GI documents of all four GIs, were eclipsed by commercial motivations for GI protection and/or current production practices. In the cases analyzed, we found some potential mismatches between GI historical claims in registration documents and actual GI cultivation and GI management practices. Conclusions: We conclude that our four GI cases do not represent “museums of production” or overly fixed perceptions of history. However, the collective action of the producer group has resulted in dynamic local cultivation practices without restricting innovation. The GI status has rather resulted in the protection of local farmers' collective action and old varieties than in the protection of old production methods.