Meagre (Argyrosomus regius) is a promising new aquaculture species, however with some bottlenecks to high-scale commercial production. One of those constraints are the scarce information about its nutritional requirements, which difficult the production of optimized diets and can lead to pathological alterations in liver, such as hepatic steatosis. Furthermore, meagre production is widely affected by granulomatosis, an infectious or non-infectious disease that may compromise fish performance and appearance. The cause of non-infectious granulomatosis is still unclear, but nutritional deficiencies are potential explanations. Since essential fatty acids are nutrients required to sustain vital functions, growth, but also immune status and disease resistance, the present work evaluated, in a 30-day feeding trial, the effect of 5 dietary n-3 long-chain polyunsaturated fatty acid levels (0.8, 1.4, 2.0, 2.6 and 3.5% in dry weight of the diet) on liver health status of meagre fingerlings. Fish fed the lowest n-3 LC-PUFA diets (0.8 and 1.4%) showed a higher hepatosomatic index, as well as a higher hepatic lipid infiltration, which resulted in severe hepatic steatosis. Oleic acid and docosahexaenoic acid were the most important fatty acids driving the variability of meagre hepatic fatty acid composition and, consequently, hepatic histological alterations. Although fatty acid composition of phospholipids was less affected by the dietary n-3 LC-PUFA, meagre fed 0.8% n-3 LC-PUFA tended to present lower levels of essential fatty acids and higher levels of oleic acid in polar lipids. Moreover, the diet with the lowest n-3 LC-PUFA content (0.8%) led to a higher incidence of hepatic granulomas, suggesting a possible relation between essential fatty acid deficiency and hepatic granulomatosis in meagre. These results suggest that the inclusion of vegetable oils in diets for meagre fingerlings should be taken with careful, guaranteeing that, at least, 2.0% DW of n-3 LC-PUFA is available in feeds, in order to maintain the normal hepatic function in meagre.