An integrative approach in mass spectrometry (MS) comprising gas chromatography coupled to MS (GC–MS), ultra-efficiency liquid chromatography coupled to MS (UPLC–MS) and easy ambient sonic-spray ionization MS (EASI-MS) is proposed for the comprehensive characterization of Amazonian oils. Coconut, andiroba and castor seed oils, which are vastly sold in markets of the Amazonian region of Brazil, were selected as a representative test set. These oils were found to contain several lipids such as triacylglycerides (TAGs), fatty acids (FAs), phytosterols and limonoids. In the analyzed samples 30 different TAGs, 11 FAs, 6 phytosterols and 7 limonoids were identified. The antioxidant capacity (AOC) of the oils, as measured by their oxygen radical absorbance capacity (ORAC), was also used to evaluate their potential biological properties as well as their possible consumption as food. Edible virgin coconut oil was the most active (0.720 ± 0.001 Trolox eq./mmol), whereas considerable lower activity was observed for andiroba and castor seed oils. The antimicrobial activities of the oils were also recorded against a panel of pathogenic bacteria and fungi in which andiroba oil was the only one that was active, solely against Enterococcus aeruginosa.