Over the past few decades, the focus on the geographic origin of cacao has shifted from Mesoamerica to the Upper Amazon region of Ecuador. Recent research clarifies the trajectory of cacao, tracing its circulation from this Amazonian origin area to the Ecuadorian coast and subsequently to Mesoamerica. However, the presence of cacao in the Andean valleys has remained elusive and largely unstudied until now. This paper presents the first evidence of cacao consumption in the Andes region at the beginning of the Integration Period (AD 500–1500) during pre-Hispanic times. Starch granules and theobromine alkaloid were identified in a vessel recovered from a settlement in present-day Quito. The high concentration of theobromine detected allows us to infer that the cacao used most likely originated from Theobroma cacao, although aDNA would be needed to confirm this. Moreover, the vessel contained starch granules from other plants, suggesting the utilization of the vessel for serving various food preparations. This finding allows us to suggest that cacao was not only consumed in the Amazon and coastal regions, but also in areas such as the current territory of Quito where cacao was not locally cultivated. The shape of the vessel in which the residue was found further suggests that the cacao was consumed as a beverage, challenging the previous belief that such practices were primarily confined to Mesoamerica. This study offers new insights into the significance of the cacao bean in pre-Hispanic societies and demonstrates how the application of various chemical methods can enhance our comprehension of historical occurrences.