The present study was applied to evaluate the effects of alternate feeding and feed restriction on gene expression, growth, proximate composition and biochemical indices in European seabass, Dicentrarchus labrax. Fish were randomly divided into six indoor tanks with 90 fish per tank in a recirculating aquaculture system. Two feeding strategies were applied, in which the first group was fed daily to satiation and the second was intermittently fed (8 days feeding to satiation–2 days starvation) for 40 days. At the end of the experiment, outlier fish were sorted as fast growers (FG) and slow growers (SG) according to their final body weight. The differential gene expression tested was related to glycolysis (pk, ldha, hk, g3pdh, eno1 and alda), fatty acid metabolism (lpl and acc) and cholesterol synthesis (7dhcr and sqle). In addition, muscle ldha and gpi expressions were positively correlated with fish weight. The concentrations of glucose, triglycerides, cholesterol and non-esterified fatty acids (NEFA) were not affected by the dietary treatments. Glucose and NEFA differed significantly between SG and FG fed groups. Overall, the physiological responses of glucose and fatty acid metabolism in fish, as recorded by gene expression assays, were triggered by minor interventions in feeding rather than the different growth rates. Expression of specific genes and biochemical parameters could be used as potential biomarkers to improve aquaculture practices and benefit fish husbandry through selective breeding, feeding strategies and farm management. The study provides new insights on the impact of intermittent feeding of European seabass, with gene markers and their potential effects, for European seabass aquaculture.