Acacia implexa, Eucalyptus rossii and Exocarpos cupressiformis are native plants of Australia, which were used by the First Peoples for medicinal purposes. In this study, 70% aqueous ethanol crude extracts were prepared from A. implexa bark and leaves, E. rossii leaves and E. cupressiformis leaves, and partitioned via sequential extraction with n-hexane, dichloromethane (DCM), ethyl acetate and ethanol. The crude extracts and fractions were screened for antioxidant activity using a novel, high-throughput lipid-based antioxidant assay, as well as the aqueous ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) assay and the Folin–Ciocalteu test for total phenols. In the lipid-based assay, non-polar n-hexane and DCM fractions showed higher antioxidant activity against the formation of peroxides and thiobarbituric acid reactive substances (TBARS) than the other fractions, whereas the non-polar fractions were not effective in aqueous assays. This illustrates that the high potential of the lipid-soluble n-hexane and DCM fractions as antioxidants would have been missed if only aqueous-based assays were used. In addition, the potent antioxidant compounds were putatively annotated using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-qTOF-MS). Gallic acid, (+)-catechin, (−)-epicatechin and tannins were found in most crude extracts.