In aquaculture facilities fish welfare could be compromised due to stressors. Fish deal with stress, inter alia, through the activation of the hypothalamic-pituitary-interrenal endocrine axis and, as a result, corticosteroids are released into the blood. Recent studies have described that corticosteroids actions depend on the specific affinities to their receptors, and the subsequent differentiated responses. Cortisol is the main corticosteroid hormone in teleost fish, being its actions dependent on the intensity and time of exposure to stressors. Short-term effects of corticosteroids are well described, but long-term effects, including changes in the energy management directly affecting growth and survival, are less understood in fish. Here we show the effects of chronic oral administration of cortisol and the synthetic glucocorticoid dexamethasone (DXM) on the intermediary metabolism of the gilthead seabream (Sparus aurata). We described a higher energy expenditure associated to both corticosteroids resulting in lower growth rates of fish. Moreover, the effects of these compounds were tissue-dependant, with differences between both hormones. Thus, cortisol-fed animals accumulated triglycerides in the liver, while DXM treatment led to glycogen storage. Cortisol and DXM stimulated amino acids catabolism and gluconeogenic pathways in muscle and gills, but the effects were significantly enhanced in DXM-fed fish. The described effects highlighted differentiated mechanisms of action associated to both corticosteroids under chronic stress conditions. Further studies should aim at describing those pathways in detail, with special attention to the functionality of glucocorticoid receptor isoforms. The effects described here for S. aurata juveniles, may serve as a basis to assess long-term stress in future comparative studies with other aquaculture species.