It has been reported that an analytical methodology combined with chemometric processing is a reliable tool for characterizing various cocoa types and their products as well as sugars and confectionery products in the context of detecting authenticity/adulteration. Considerable attention has been given to the multivariate classification of multielemental and/or stable isotope ratio profiles. It is important to determine the potential influence of different parameters on the quality of cocoa beans, chocolate and other natural sweeteners. Analytical methods coupled with chemometric tools can be useful approaches for identifying interspatial or intervarietal adulterants and the addition of adulterants to different natural sweeteners, for the detection of sugarcane impurities, and for evaluating the degree of pollution within cultivation areas. Distinguishing between conventionally and organically cultivated cocoa beans or identifying various steps of the chocolate manufacturing process or different sugar plant products, i.e., from raw sugarcane to by-products, has been possible during each progressive industrial step. Accurate results enable the identification of falsely labelled products and hence preserve brand reputations.