This study evaluated the effects of dietary fortification of high plant protein aquafeeds with two microalgae-based functional ingredients on growth, muscle composition, oxidative status, digestive function, and intestinal morphology in juvenile Sparus aurata with an average body weight of 28.4 g. Four diets were tested: a control with high fishmeal and fish oil (CTF), a plant-based diet containing 5% fishmeal and 5% fish oil (CTV), and two CTV diets supplemented with 1% LB-IMMUNOboost (IB10) or 1% LB-LIVERprotect (LP10). Fish fed CTV and LP10 showed reduced growth compared to CTF, while IB10 partially mitigated these effects. High plant dietary inclusion reduced muscle protein and increased lipid content, except in IB10-fed fish. Reduction in fishmeal and fish oil decreased muscle saturated fatty acids, EPA, and DHA. Despite similar HUFA levels in the plant-based diets, IB10 and LP10 significantly reduced lipid peroxidation, indicating a direct antioxidant effect of the functional ingredients. Digestive enzyme activities were impaired in CTV-fed fish but partially recovered in IB10 and LP10, particularly IB10. Histology revealed shorter intestinal folds and more goblet cells in high plant protein diets, especially LP10, potentially impairing absorption. Overall, microalgae-based functional ingredients, particularly LB-IMMUNOboost, partially alleviated these adverse effects, supporting their use in more sustainable aquafeed formulations.