The cocoa botanical and geographical origin and the primary processing steps applied by cocoa farmers at the beginning of the supply chain influence the chemical compositional traits of the cocoa beans. These features are carried along the supply chain as intrinsic markers up to the final products. These intrinsic markers could be used for tracking and tracing purposes. In this study, we examined the retention and loss of compositional signatures from cocoa beans to chocolates. Volatile, elemental and stable isotope signatures of cocoa beans of 10 different origins and 11 corresponding chocolates were determined by high sensitivity-proton transfer reaction-mass spectrometry (HS-PTR-MS), inductively coupled plasma-MS (ICP-MS) and isotope ratio-MS (IR-MS), respectively. The volatile fingerprints provided mostly information on the origin and primary processing traits of the raw cocoa beans in the chocolates. Volatile compounds that are relevant markers include: acetic acid (m/z 61), benzene (m/z 79), pyridine (m/z 80), 2-phenylethanol (m/z 123), and maltol (m/z 127). On the other hand, the elemental and stable isotope characteristics are more indicative of the cocoa content and added ingredients. Possible elemental markers for cocoa origin include Fe, Cr, and Cd. VOCs appear to be the most robust markers carried from cocoa beans to chocolates of the groups examined. This provides the potential for track and trace of cocoa beans from farm to chocolates.