The aim of this study was to evaluate the effects of alternate feeding schedules, in which diets with different lipid sources were alternated, on fatty acid profile, accumulation of long chain omega-3 polyunsaturated fatty acids (n-3 LC-PUFA) and expression of selected fatty acid bioconversion genes in European sea bass juveniles. Five treatments were administered to fish; fish oil treatment (FO; continuously fed a fish oil (FO)-diet), canola oil treatment (CO; continuously fed a canola oil (CO)-diet), blend oil treatment (BLD; continuously fed with a diet containing both FO and CO), alternate schedule treatment (AST; fish fed for 3 weeks with CO and the following 3 weeks with BLD), and finishing schedule treatment (FST; fish fed for 9 weeks with CO and the following 3 weeks with FO) for 12 weeks. Significantly higher SGR and lower FCR were detected in fish fed the FO, BLD and FST diets compared to those fed with CO and AST diets. As expected, the n-3 LC-PUFA accumulation (mainly EPA and DHA) was generally decreased in the whole body, flesh and liver in the CO fish compared to FO fish. Although the FST and AST fish consumed the same quantity of fish oil and canola oil throughout the experimental period, the proportion of n-3 LC-PUFA in the flesh of the FST fish was significantly higher than in the AST fish, confirming the major effect of the fish oil intake at the final stages (3 weeks) of the experiment. Moreover, no significant effects were detected at the molecular level for hepatic transcriptional factors involved in the regulation of the fatty acid bioconversion metabolic pathway (peroxisome proliferator activated receptors-alpha; PPAR alpha and sterol regulatory element binding proteins-1; SREBP1), or in the key enzymes involved in fatty acid bioconversion (D6-desaturase enzyme; D6D and fatty acid elongases; ELOVLs) across all treatments, suggesting that the n-3 LC-PUFA level in sea bass cannot be modified through increased fatty acid bioconversion capacities in the liver (at least a molecular level). In conclusion, a nutritional modulation of n-3 LC-PUFA content in flesh was observed in relation to the feeding schedules independently to modifications of the fatty acid bioconversion capacities.