Several species of microalgae are promising as an alternative source of omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA). Photoautotrophic species show the greatest potential, since incorporating them into food products leads to oxidatively stable products; however, the presence of photosensitizers could reduce the shelf-life due to the appearance of photo-oxidation on exposure to light. This study investigated the oxidative impact of illumination for aqueous model suspensions enriched with Phaeodactylum (phototrophic microalgae─containing potential photosensitizers) and Schizochytrium (heterotrophic microalgae─lacking photosensitizers) during storage for 28 days at 37 °C. Primary (peroxide value) and secondary (volatiles with gas chromatography (GC)-mass spectrometry) oxidation products, n-3 LC-PUFA content (GC), and pigments (high-pressure liquid chromatography) were assessed. The results showed that photo-oxidation did not cause oxidative instability for Phaeodactylum samples compared with strong autoxidation in Schizochytrium samples. For the Phaeodactylum-enriched suspensions, only minimal photo-oxidation could be detected and the n-3 LC-PUFA content remained stable throughout storage regardless of illumination.