Fish are ectotherms and this means they are highly vulnerable to changes in ambient temperature, particularly during early developmental stages when temperature can induce persistent effects on phenotypic traits. In this study, the effect of egg incubation temperature on the response of juvenile European sea bass (Dicentrarchus labrax) to food deprivation and recovery after refeeding was assessed. Eggs were incubated at 11, 13.5 and 16 °C until hatching and then were reared at a common temperature until 9 months when fish were deprived of food for one week. The recovery from food deprivation was evaluated at 10 h and 2 days post-refeeding. Food deprivation in fish from eggs incubated at the highest temperature (16 °C) compared to 11 and 13.5 °C exhibited the most morphological and metabolic changes in the liver and foregut. Liver metabolism was changed as revealed by the significant reduction in lipid area and the increased number of hepatocyte nuclei. Foregut atrophy was coupled to a significant up-regulation of transcripts associated with gluconeogenesis (pck1) and peptide absorption (pept1). A modified metabolic response to the fast-refeed regime was revealed by the significantly decreased levels of plasma lactate, which may result from up-regulation of transcripts of the thyroid axis, deiodinase 2 (dio2) in the foregut. Fish incubated as eggs at a lower temperature (11 °C) exhibited less changes following the fast-refeed regime. Food deprivation did not significantly modify the morphology of the foregut and the liver parenchyma recovered sooner in fish from the 11 °C egg thermal regime compared to fish from the other thermal regimes following refeeding. The latter group of fish had a temporary stimulation of the GH-IGF axis with significant up-regulation of liver insulin-like growth factor I and II (igf-1 and igf-2) after fasting. The liver parenchyma of fish from the 13.5 °C egg thermal regime (the standard temperature of the hatchery stage) did not recover by the end of the experiment and transcripts of catalase (cat), encoding an antioxidant enzyme, were significantly downregulated compared to fish from the other egg thermal regimes. Our results suggest that thermal imprinting at the egg stage in European sea bass modified the juvenile metabolic response to food deprivation and the recovery response when feeding was resumed.