Testing the composition, quality and authenticity of edible oils is crucial to safeguard the consumers’ rights and health. The aim of our study was to identify oil-specific markers to enable the differentiation and authentication of sunflower, sesame, flaxseed and rapeseed oils, and to evaluate their antioxidant activity, total phenolic and carotenoid content. A metabolomic approach based on liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry was employed for marker discovery. Spectrophotometric method was used for determination of antioxidant activity, total phenolic and carotenoid content. 76 oil samples from the four different manufacturers were examined. We identified 13 oil-specific markers for sunflower seed oil, 8 for rapeseed oil, 5 for sesame seed oil and 3 for flaxseed oil, their retention times, accurate masses, and characteristic fragment ions are reported. The abundances of the markers for each plant species were found to vary depending on the oil producer and the product batch. Significant differences in antioxidant activity, total phenolic and carotenoid content were also observed both between oils and within oil type. The highest total phenolic content (84.03 ± 4.19 to 103.79 ± 3.67 mg of gallic acid/kg) and antioxidant activity (245.67 ± 7.59 to 297.22 ± 2.32 mg Trolox/kg) were found in sesame seed and flaxseed oils, respectively. Identified metabolic markers can be used as qualitative markers to confirm the authenticity or to detect adulterations of oils. Composition, properties and authenticity testing should be more rigorous for food products marketed as health-promoting.