The purpose of this study was to check if it is possible to influence sea bass juvenile metabolism by a conditioning of larvae from day 6 post hatching to day 45 to a low or a high HUFA compound diet (LH, 0.8% EPA + DHA and HH, 2.2% EPA + DHA) when reared at 16 or 22 °C. Following a 3-month intermediate period (at 19 °C using a commercial diet), the adaptability of the 4 initial larval groups to a HUFA experimental deprived diet (0.5% EPA + DHA) were tested at 19 °C in a 60 day-experiment (d-151–211). The four experimental duplicated conditions were ex-LH16 and ex-HH16 for the 2 groups previously reared at 16 °C (initial weight, 7.3 ± 0.5 g) and ex-LH22 and ex-HH22 for the 2 groups previously reared at 22 °C (initial weight, 11.1 ± 0.5 g). Survival was maximal and there was a 1.6–2 fold increase in mass during the experiment. Growth was similar in the 4 experimental groups: NS difference in growth curve slopes (P = 0.7). At the end of the experiment (d-211), whole body fat levels were in the same range in all groups (13–15% WW). The fatty acid (FA) composition in polar lipids (PL) and total lipids (TL) were significantly affected by initial weight related to larvae conditioning, which can be mainly attributed to a dilution effect (impact of initial FA content on final FA content versus relative mass increase during the course of the experiment). Conversely to this trend, DHA content in PL was higher in the ex-LH groups than in the ex-HH groups whatever thermal conditioning of larvae was. This indicated that ex-LH groups had a better capacity to adapt to a deficient HUFA diet than ex-HH fish. The relative expression of the delta-6 desaturase (Δ6D) was significantly higher in ex-LH than in ex-HH groups (P < 0.001) between d-151 and d-181, which suggested that Δ6D transcription in ex-LH groups was positively modulated by the HUFA-deprived diet. This stimulation of the first step of the desaturation/elongation pathway could allow synthesizing FA needed to compensate low dietary HUFA supply. This study shows for the first time that it seems possible to influence juvenile fish metabolism by a nutritional conditioning during the larval stage.