The objective of this study was to determine whether supplementation with deficient zinc (Zn) or/and excess copper (Cu) in the first-feeding diet of rainbow trout fry influenced the growth and physiological regulation of juvenile fish subjected to similar challenge feeds again. The feeding trial lasted for 24 weeks and had three phases. In phase I, rainbow trout fry was treated with one of four different plant-based feeds containing or exempting Zn or Cu supplementation (coded Zn-Cu-, Zn+Cu-, Zn-Cu+, Zn+Cu+) for 6 weeks. Thereafter, all groups were fed a common commercial feed for the next 12 weeks (phase II). In phase III, all groups were fed with the “challenge diet” for another 6 weeks which was the basal diet (Zn-Cu-) except that the vegetable oils were replaced by fish oil. The results demonstrated that fish fed a Zn+ diet at first feeding increased larval growth (phase-I), but it had no effect on growth at the end of phase II when fed commercial feeds. In phase III, when re-introduced to a Zn- challenge diet, the feed intake and growth of juveniles with Zn+ history significantly increased, with reduced feed efficiency. Fish growth was neither influenced by dietary Cu levels or by the dietary Cu history in any of the growth phases, but dietary Cu excess (Cu+) reduced body lipid and energy content in fry. In phase I, lower whole-body Zn concentration was observed in the fry of Zn- group compared to Zn+, while the contrary was observed in the juvenile fish as affected by dietary Zn history (phase III). In addition, Zn- dietary history showed increased levels of PUFA and higher mRNA expression of fatty acid biosynthesis genes in the liver. To conclude, early-stage dietary Zn+ history improved growth of juvenile rainbow trout, while dietary Zn- history exhibited signs of improved fatty acid biosynthesis capacity in the liver.