The aim of this work was to evaluate two functional feeds for the gilthead seabream, Sparus aurata, containing low inclusion of two microalgae-based products (LB-GREENboost, LBGb; and LB-GUThealth, LBGh). Fish (12-13 g) were fed for 13 weeks a control diet or one of the four diets supplemented with both products at 0.5% or 1%. LBGb and LBGh did not affect specific growth rate or survival, but increased feed efficiency by decreasing feed intake and enlarging the intestines. LBGb increased hepatosomatic index and reduced cortisol levels in plasma, while both products lowered plasma lactate. Extensive metabolite and metabolic enzyme profiling revealed that microalgae supplementations, especially 1% LBGh: (i) decrease plasma lactate and increase hepatic glycogen, (ii) reduce hepatic gluconeogenesis, (iii) enhance hepatic lipogenic activity and lipid secretion, (iv) led fish to double triglyceride content in muscle and to stimulate its lipid oxidative capacity, and (v) increase the content of monounsaturated fatty acids and the omega-3 alpha-linolenic acid in muscle. This study demonstrates that both microalgae-based products are suited to improve feed efficiency and orchestrate significant changes in the intermediary metabolism in gilthead seabream juveniles.