The volatile and non-volatile chemical composition and bioactivity of propolis from the species Apis mellifera has been widely studied, but there is very little knowledge regarding propolis of other bee species, which ultimately hinders their differentiation and potential use. In this work, 53 propolis samples of A. mellifera and four stingless bee species (Frieseomielitta sp., Melipona eburnea, Melipona sp., and Trigona sp.) were collected in Colombia. An electronic nose with 10 metal oxide semiconductor sensors (MOS) was used to generate a pattern of the representative volatile compounds of the samples. Ethanolic extracts were obtained to assess their antioxidant activity towards DPPH radical and ABTS radical cation, total phenolics, and color (CIELAB space). The results showed an overall similarity of the aromatic profiles between species. The antioxidant activity of Frieseomielitta sp. propolis was higher than that of A. mellifera and the other species, in correspondence with a higher phenolic content. CIELAB color parameter b* was the most differentiating variable among samples, indicating a variation of propolis colors between red and yellow. By combining the data from physico-chemical analysis and aromatic profile, it was possible to differentiate the propolis from each bee species, with the exception of those from Melipona sp. and Trigona sp., indicating their similarity. These results have practical significance since they are a starting point to recognizing and valuing native stingless bee propolis and their bioactive potential, which, in addition to geographical differentiation and further quality parameters evaluation, will enhance their commercial exploitation.