Global climate changes have led to a depletion in omega-3 polyunsaturated fatty acids (n-3 PUFA) in marine phytoplankton that—with food web transfers—could negatively impact fish performance. The aim of this study was to assess the effect of a reduction in the dietary availability of n-3 PUFA on growth performance, organ allometry, and fatty acid composition in juvenile European sea bass (Dicentrarchus labrax) raised at two different temperatures: 15 °C (natural conditions) and 20 °C (global warming scenario). Fish were fed for 5 months with two isoenergetic and isoproteic diets: a reference diet (RD; 1.65% n-3 PUFA on a dry matter basis, DM) used as a proxy of trophic networks where n-3 PUFA were plentiful, and a lower n-3 PUFA diet (LD; 0.73% n-3 PUFA on DM) designed to mimic the expected decrease in n-3 PUFA sources resulting from global climate changes. Results showed decreasing growth rates and slight changes in the muscle polar lipid profile in LD-fed sea bass juveniles, whereas neutral lipids were more affected over the long term. The relative masses of the heart and gastrointestinal system were higher at 20 °C, while liver mass was higher at 15 °C in LD-fed juveniles. However, the mesenteric fat of RD-fed juveniles was higher at 15 °C. Altogether the results suggest that sea bass juveniles are able to implement physiological mechanisms to cope with a decrease in dietary n-3 PUFA and are able to improve growth at the higher temperature, even with a decreased availability of n-3 PUFA. The temperature-driven increase in growth is also observed under the restricted n-3 PUFA diet, and this is accompanied by significant effects on organ allometry and FA profiles. This may indicate the presence of some metabolic costs that remain to be evaluated, but which illustrate that the combination of warming temperatures and n-3 PUFA depletion has significant effects on life history traits.