The application of appropriate analytical methods is useful for evaluating the nutritive quality of food. The determination of mineral components and stable isotopic ratios is important for the classification of honey of various origins, i.e. geographical and botanical aspects. Moreover, other analytes, e.g. sugars, organic acids, phenols and flavonoids, can also be considered together with both abovementioned analytes. Among the commonly recommended analytical tools, the most preferred are AAS with four techniques, i.e. FAAS, ET–AAS, CV–AAS and HG–AAS, as well as HR–ICP–MS, Q–ICP–MS, ICP–MS, ICP–AES and ICP–OES assisted by the use of chemometric analysis, e.g. PCA, FA, HCA, LDA, DFA, ANN, PLS–DA and PLSR. Moreover, the combination of analytical and multivariate tools is powerful for the classification of honeys in terms of variety, the degree of environmental pollution and the ability to detect fraud to preserve the brand reputations of original food products. The data obtained provide a deeper understanding of the principles of the elemental composition of foods in the case of the risks to human health resulting from the consumption of falsely-labelled food products.