The growing health consciousness of consumers has led to an increase in the consumption of artisanal chocolates, mainly due to their recognized health benefits. However, processing steps such as fermentation and drying of cocoa beans can favor the growth of ochratoxigenic fungi. This study aimed to assess the occurrence of ochratoxin A (OTA) in cocoa beans (purchased from e-commerce and post-harvest processing) and bean-to-bar chocolates sold in Brazil. An HPLC-FLD method was validated, with recovery values between 84 and 97% and limits of detection and quantification of 0.04 and 0.01 µg/kg, respectively. OTA was detected in 30% of the cocoa bean samples studied (n = 43), with values ranging from < 0.04 to 1.18 µg/kg. Regarding the bean-to-bar chocolates (n = 62), the OTA concentrations ranged from < 0.04 to 1.11 µg/kg, with a prevalence in semi-sweet and dark chocolates. Despite representing a growing market, to the best of our knowledge, this is the first study to report OTA concentrations in bean-to-bar chocolates and Brazilian cocoa beans used to produce this type of chocolate.