The occurrence of ochratoxin A (OTA) and OTA-producing fungi in cocoa beans has been previously reported to be linked to harvest and post-harvest treatment conditions. The aim of this study was to identify OTA-producing fungi and OTA prevalence during harvest, fermentation, drying and storage of cocoa beans from two farms located in Mexico. Ochratoxin A analyses were performed with immunoaffinity columns and detection by high performance liquid chromatography. A high level of ochratoxigenic fungi contamination was observed during drying (78.4% ± 13.6) and storage (70.3% ± 3.2) in cocoa samples from farm A. In farm B, the washing process of cocoa beans after fermentation reduced pulp residues and consequently, diminished the OTA-producing fungi infection during drying (12.7% ± 5.8) and storage (37% ± 10.4). The main OTA-producing strain isolated from Malt Extract Agar (MEA) growth medium was Aspergillus carbonarius (14,300 µg/kg). The prevalence of ochratoxigenic species was correlated with high levels of OTA beans during storage of cocoa beans from both farms A and B (305 ± 15.0 and 11.3 ± 0.5 µg/kg, respectively) and in fresh cocoa beans from farm B (22.2 ± 3.5 µg/kg). To the best of our knowledge, this is the first time OTA content and ochratoxigenic fungal species during cocoa processing has been reported. This allowed the identification and assessment of the sanitary risks linked to cocoa bean processing.