A survey was conducted on two Brazilian chocolate manufacturing companies (A and B) to investigate/determine Enterobacteriaceae, coliforms and Salmonella contamination. Samples of different chocolate types, processed cocoa-based ingredients, manufacturing environment, and workers' hand surfaces were analyzed. Salmonella and Escherichia coli were not detected. However, in 25.8% of the chocolate samples, Enterobacteriaceae were isolated while total coliforms were detected in 13.3%. Among the processed cocoa-based ingredients, two samples of cocoa liquor showed contamination by Enterobacteriaceae and total coliforms, and in one sample thermotolerant coliforms were also recovered. For equipment and utensils, Enterobacteriaceae were isolated in around 25.4% of the samples, whereas total coliforms were detected in 10.2%. Moreover, in company A 14.3% of manufacturing environment samples were contaminated by thermotolerant coliforms. The food handlers from both companies showed a high percentage of Enterobacteriaceae contamination on their hands. The results showed that the manufacturing environment including food handlers was considered the most likely Enterobacteriaceae contamination source of the finished product. These data also highlight Enterobacteriaceae as a good hygiene indicator for the chocolate industry. •Identification of the Enterobacteriaceae contamination source in chocolate.•Cocoa-based ingredients were not a significant contamination source in chocolate.•Processing environment was the most likely Enterobacteriaceae source in chocolate.