The aim of this research was to examine the influence of pasteurisation of cocoa liquor at different temperatures (115, 120, 125 and 140 °C) and 3-week-storage time at 40 °C on microbial safety, peroxide value, polyphenol, and flavan-3-ol content. Peroxide value of the cocoa liquor increased after both, pasteurisation and storage, but not significantly. Although total polyphenol content decreased, flavan-3-ol content was stable during the investigated period. Microbial quality was satisfying, and the most stable mass was the one treated at 140 °C.