Nutritional programming is a promising concept for promoting metabolic adaptation of fish to challenging conditions, such as the increase in water temperature. The present work evaluates in ovo arginine or glutamine supplementation as enhancers of zebrafish metabolic or absorptive capacity, respectively, at optimum (28 ºC) and challenging temperatures (32 ºC) in the long-term. Growth performance, free amino acids profile, methylation index and the activity levels of digestive and intermediary metabolism enzymes were analysed to assess the metabolic plasticity induced by an early nutritional intervention. Temperature affected fish larvae growth performance. At the end of the experimental period 28 ºC-fish showed higher dry weight than 32 ºC-fish. The effects of the early supplementation were reflected in the larval free amino acids profile at the end of the experiment. Higher methylation potential was observed in the ARG-fish. In ovo amino acid supplementation modulated the metabolic response in zebrafish larvae, however, the magnitude of this effect differed according to the amino acid and the temperature. Overall, arginine supplementation enhanced carbohydrates metabolism at 32 ºC. In conclusion, the present work suggests that in ovo arginine supplementation may promote a better adaptive response to higher temperatures.