The effect of dietary short-chain fructooligosaccharides (scFOS) incorporation on growth, feed utilization, body composition, plasmatic metabolites and liver activity of key enzymes of lipogenic and amino acid catabolic pathways was evaluated in gilthead sea bream reared at 18 and 25 °C. Four practical diets containing plant ingredients and fish meal (50:50) as protein sources and supplemented with 0, 0.1, 0.25 and 0.5 % scFOS were fed to triplicate groups of fish for 8 weeks. Growth performance, feed efficiency and nitrogen retention were higher at 25 °C. In fish reared at 18 °C, there was a positive correlation between dietary scFOS concentration and growth. At 18 °C, liver glycogen was higher in fish fed the control diet, while at 25 °C it was higher in fish fed the 0.5 % scFOS diet. Plasma cholesterol LDL was lower in fish fed 0.25 % scFOS diet, and in fish reared at 18 °C plasma glucose was higher in fish fed the 0.1 % scFOS diet. Glucose 6-phosphate dehydrogenase, fatty acid synthetase and aspartate aminotransferase (ASAT) activities were higher in fish reared at 18 °C, whereas alanine aminotransferase activity was higher in fish reared at 25 °C. scFOS affected ASAT activity, which was lower in fish fed 0.25 % scFOS diet. Although, scFOS seemed to have no major effects on gilthead sea bream metabolism, the positive correlation between dietary prebiotic incorporation and growth at 18 °C indicates a beneficial effect of scFOS in fish reared at low temperatures.