The use of microalgae as a sustainable source of n-3 long-chain polyunsaturated fatty acids (LC-PUFA) as an alternative to fish oils from small pelagic fish (e.g., anchovy, sardine) has received growing interest in the past few years. The present study aimed to: (i) produce Aurantiochytrium mangrovei biomass by heterotrophic fermentation using a medium containing anaerobic digestion liquid effluent, and (ii) evaluate a biomass rich in n-3 LC-PUFA and good quality proteins as a feed ingredient for sea bass juveniles and larvae. Two 800 L bioreactors were used to produce Aurantiochytrium biomass in non-axenic conditions. Biomass was then filtered through a crossflow filtration system (300 Kda ceramic membrane) and freeze-dried. Sea bass juveniles (32.7 ± 4.2 g) were fed both a control diet and a diet containing 15% of freeze-dried A. mangrovei biomass for 38 days. Juvenile survival percentage was 90% on average in both dietary conditions. Similar growth was observed between fish fed with both diets, demonstrating the feasibility to replace 15% of a standard fish feed by Aurantiochytrium biomass. The liver of sea bass juveniles fed with the A. mangrovei diet contained significantly higher proportions of 22:6n-3, 22:5n-6, and 20:4n-6 than those fed with the control diet, while the proportions of 16:0, 16:1n-7, and 18:1n-9 were significantly lower. The secondary oxidation, as measured by malonylaldehyde (MDA) content, in the liver and muscle of juveniles fed with the microalgae diet tended to be higher than in fish fed the control diet, but the differences were not statistically significant. Although the larvae survival percentage was low for all the tanks after 41 days of rearing, the inclusion of 15% of hydrolyzed A. mangrovei biomass in the larvae micro-diet did not impair the development of sea bass larvae and only marginally affected their lipid composition. In the future, we have to further optimize a sustainable workflow between Aurantiochytrium cultivation and fish feed production and confirm the zootechnical and biochemical results.