This study assessed the natural occurrence of Ochratoxin A (OTA) in quinoa (Chenopodium quinoa Willd.) of the Chimborazo ecotype, cultivated in the Ecuadorian Andes. A total of 49 samples were analyzed using a validated high-performance liquid chromatography with fluorescence detection (HPLC-FLD) method, achieving a detection limit of 1.72 µg/kg, including the uncertainty of the method. Results revealed that 48 samples (98%) were below the detection limit, confirming compliance with international food safety standards. However, one isolated sample contained 51.38 µg/kg of OTA, surpassing regulatory limits. Interestingly, this contaminated sample exhibited lower moisture content than other uncontaminated samples, suggesting that OTA formation is influenced by factors beyond moisture levels. These include fungal spore presence, mechanical damage to the grain, nocturnal condensation, and localized microclimates at the field level, which may promote OTA biosynthesis prior to laboratory analysis. This study underscores the importance of implementing comprehensive control measures across the production chain—from pre-harvest management and harvesting practices to post-harvest handling—to minimize OTA contamination risks. Moreover, these findings highlight the need for continuous monitoring and application of best agricultural practices to ensure quinoa quality and safety, safeguarding its global market competitiveness.