Stingless bee honey (SBH) is gaining attention due to its nutritional, sensorial, and medicinal characteristics. This study focuses on the combination of physicochemical properties, antioxidant capacity, mineral profile, and mass spectrometry-based fingerprints, using a chemometric approach to differentiate SBH (n = 18) from three different Brazilian biogeographical zones (Caatinga, Cerrado, and Atlantic Forest). The physicochemical properties of SBH varied, resulting in a wide range of water activity, moisture, total soluble solids, pH, and total and free acidity. The Caatinga honey showed the highest and the lowest contents of phenolics and flavonoids, respectively. The antioxidant free-radical scavenging assays demonstrated that the Brazilian SBH has a high antioxidant potential. The mineral profile of honey samples from the Atlantic Forest revealed higher contents of Ca and Fe while the Cerrado and Caatinga honey showed the highest P contents. Partial Least-Squares Discriminant Analysis (PLS-DA) analysis separated the samples into three groups based on the biogeographical zones of harvest. The main separation factors between groups were the m/z 326 ion and the Fe content. Univariate analysis confirmed that Fe content is important for SBH discrimination. The present results indicate that the origin of SBH can be determined on the basis of mineral profile, especially Fe content.