Oxidation of n-3 PUFA-rich oils in the gastrointestinal (GI) tract leads to the formation of potentially harmful compounds such as 4-hydroxy-2-hexenal (HHE), 4-hydroxy-2-nonenal (HNE), and malondialdehyde (MDA). This study investigated the interplay between fatty acids release, tocopherol concentration, and formation of hydroperoxides, HHE, HNE, and MDA during simulated digestion of Schizochytrium sp. oils, in comparison with cod liver and linseed oils. Free DHA showed a stronger correlation with tocopherol consumption than esterified DHA. Hydroperoxide formation showed non-linear relationship with tocopherol amounts and free PUFAs, though also bound PUFAs correlated to hydroperoxide formation. Key fatty acids explaining increases in oxidation markers other than DHA, such as 20:3n-6, were identified. While HHE formation correlated with oil unsaturation and esterified DHA, MDA had linear relationship with hydroperoxide formation. These findings enhance the understanding of lipid oxidation mechanisms during digestion, providing valuable insights for improving the stability of n-3-rich oils in food applications.