Chicha is a traditional ethnic corn-based fermented beverage with a profound cultural relevance in the Andean region, especially in Peru where it has been part of religious ceremonies since pre-Inca civilizations. Chicha de Guiñapo is made with purple corn and is a typical beverage from the Peruvian region of Arequipa (South of Peru) where some local people still preserve its traditional process and use, but no investigation has been focused on the study of its potential health-relevant functional properties linking the historical perspectives. The current research was aimed at advancing the ethnic cultural relevance of this traditional beverage with an understanding of deep historical and ecological roots and further by evaluating the differences in the traditional processing of Chicha de Guiñapo from five geographical zones in Arequipa (Peru). Furthermore, to understand the potential health relevance, the influence on the total phenolic content (TPC), the total anthocyanin content (TAC), the antioxidant capacity, the in vitro inhibition of α-glucosidase and α-amylase relevant for hyperglycemia management, along with the physicochemical characteristics, were evaluated. No significant differences were observed in the physicochemical parameters, the antioxidant capacity, and the phenolic contents among the Chicha samples from different origins. However, all samples showed a remarkable in vitro inhibition of α-glucosidase and α-amylase with a significant influence of the geographical zone of origin that links historical usage and contemporary health benefits. The Z2 Chicha sample that followed the most traditional preparation had the highest values of TAC, in vitro antioxidant capacity, and anti-hyperglycemia-relevant α-glucosidase and α-amylase inhibitory activities. Results from the current study reveal that Chicha has an important health-relevant functional potential and that the preservation of the traditional historical and ethnic knowledge about its processing is critical for its validation for wider use across all communities.