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Cocoa is a concentrated source of dietary flavanols—putative bioactive compounds associated with health benefits. It is known that fermentation and roasting reduce levels of native flavonoids in cocoa, and it is generally thought that this loss translates to reduced bioactivity. However, the mechanisms of these losses are poorly understood, and little data exist to support this paradigm that flavonoid loss results in reduced health benefits. To further facilitate large-scale studies of the impact of fermentation on cocoa flavanols, a controlled laboratory fermentation model system was increased in scale to a large (pilot) scale system. Raw cocoa beans (15 kg) were fermented in 16 L of a simulated pulp media in duplicate for 168 h. The temperature of the fermentation was increased from 25–55 °C at a rate of 5 °C/24 h. As expected, total polyphenols and flavanol levels decreased as fermentation progressed (a loss of 18.3% total polyphenols and 14.4% loss of total flavanols during fermentation) but some increases were observed in the final timepoints (120–168 h). Fermentation substrates, metabolites and putative cocoa bioactive compounds were monitored and found to follow typical trends for on-farm cocoa heap fermentations. For example, sucrose levels in pulp declined from >40 mg/mL to undetectable at 96 h. This model system provides a controlled environment for further investigation into the potential for optimizing fermentation parameters to enhance the flavanol composition and the potential health benefits of the resultant cocoa beans. Published version