Germination of seeds is known to affect the nutritional composition of cold-pressed oils. This study focused on the effects of germination on the antioxidants and oxidative stability of linseed and sunflower seed oil. As hypothesized, germination led to increased antioxidant activities and tocopherol, chlorophyll and carotenoid content. Analysis revealed a 37.2 ± 3.5-fold and 11.6 ± 1.5-fold increase in polyphenol content in linseed and sunflower seed oil from germinated seeds, respectively. Using LC-HRMS/MS, profiles with up to 69 polyphenolic substances were identified in germinated seed oils for the first time. Germination promoted lipid hydrolysis, as evidenced by NMR, with overall significant decreases in triacylglycerol content leading to increased diacylglycerol and free fatty acid values. Rancimat measurements predicted a 4.10 ± 0.52-fold longer shelf-life for germinated linseed oil. This study successfully demonstrated the potential of germination to develop PUFA-rich oils with enhanced antioxidant capacity and oxidative stability. Display omitted •Germination significantly increased antioxidants in linseed and sunflower seed oils.•Up to 69 phenolic substances from germinated seeds oils were identified by LC-MS/MS.•Rancimat predicted 4.10 ± 0.52-fold longer shelf-life in germinated linseed oil.•NMR revealed significant increase in FFA of 13.46 ± 0.6% in germinated linseed oil.