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The low oxidative stability of polyunsaturated fatty acids (PUFA) in omega-3 supplements may cause the formation of compounds that may have negative healthy effects. Extra virgin olive oil (EVOO) contains high content of monounsaturated fatty acids (MUFA) and polyphenols, which might improve PUFA oxidative stability when combined with vegetable oils enriched in them. In order to prevent the formation of oxidized compounds and improve the shelf-life of PUFA, different proportions of EVOO (enriched in oleic acid and polyphenols) and algae oil (AO) were studied. For this purpose, both pure oils combined in different proportions were stored under accelerated degradation conditions (40 and 55 °C) for 70 days. Correlations and significant changes in levels of fatty acids composition, phenolic components and oxidation rates during storage time were studied. Throughout storage, higher EVOO quantity at the final mixture was related with less PUFA degradation, where a 27.53% decrease in PUFA of AO passed to less than 12% in a resulting oil of at least 75% of EVOO. PUFA concentration correlated with the formation of secondary peroxides, while MUFA content from EVOO produced a reduction in PUFA degradation. In addition, high secoiridoid levels in mixtures decreased the hydrolysis of triglycerides over the time.