The potential ingestion of food products contaminated with ochratoxin A (OTA) is cause of concern for public health. Currently, several detection methods are available to detect OTA in singles spices but not in spice mixtures such as merkén. The present study modified, optimized, and validated a method for successful OTA quantification in merkén, paprika, and chili. A total of 321 merkén (n: 256), paprika (n: 39), and chili (n: 26) samples were collected from different retail locations in Chile over a 5-year period (2016–2020). OTA levels were determined by high performance liquid chromatography with fluorescence detection (HPLC-FLD). Validation parameters that included the limit of detection (LOD: 0.3 ng g−1), limit of quantification (LOQ: 1.0 ng g−1), linearity (0.9975), recovery in a fortified blank matrix (5 ng g−1: 81–105%), and relative standard deviation (RSD: 0.49–6.87%) were satisfactory. The presence of OTA in merkén, paprika, and chili samples was 66%, 59%, and 61%, respectively. Maximum OTA levels in merkén, paprika, and chili exceeded the limit established by national regulations of 5 ng g−1 by 77-fold (387.9 ng g−1), 59-fold (297 ng g−1), and 14-fold (71.6 ng g−1), respectively. The estimated daily intake (EDI) values were considerably higher in 2017 than 2020 (paprika ˃ chili ˃ merkén). The EDI values were also lower than the Benchmark dose level (BMDL10; 4730 ng kg−1 bw day) for non-neoplastic effects. Our study pinpointed the importance for continuously monitoring and regulating the OTA contamination in agricultural commodities such as spices. More investigations should be generated to modify the current regulation of OTA in spices.