Using a detailed HPLC–ESI-MS analysis including both high resolution and tandem MS analysis, a series of fourteen novel flavonoids were identified from alcoholic extracts of raw fermented cocoa beans from Cameroon. The novel compounds include a series of isomeric hexosides of flavan-3-ols and novel proanthocyanidine dimers and trimers and a sulfated flavan-3-ol. Additionally a jasmonic acid sulfate derivative was identified in the cocoa bean extracts as one of the major metabolites produced under fermentation stress. Therefore, the chosen HPLC–ESI-MS analysis method revealed a greater complexity of the cocoa bean polyphenolic extract than previously reported and allowed individual assignment of novel compounds.