Genetic selection and novel raw materials for aquafeeds are current key tools in the ongoing effort to increase the productivity, efficiency, and sustainability of the aquaculture sector. Selective breeding could also improve the utilization of novel dietary formulations with emergent ingredients. Gilthead sea bream juveniles, either coming from a selective breeding program based on growth traits, or a non-selected population, were nutritionally challenged with two novel dietary formulations that were compared with a Control diet based on 15% FM and 6% FO dietary commercial levels for this species. The novel formulations included an insect meal diet (INS) at 5% of the diet to replace 33.3% of the dietary FM, or a single-cell protein diet (SCP) at 10% of the diet and to replace 66.7% of the dietary FM. Fish oil was also totally replaced in these diets by a blend of poultry oil and Veramaris algal oil. Better growth and feed utilization of the selected genotype compared to non-selected fish was observed, at any of the diets assayed. INS and SCP novel diets reduced general performance of fish by reducing feed intake. However, selected fish fed novel diets showed very similar growth and lower feed conversion ratio compared with non-selected fish fed a control diet. The novel formulations increased n-3 LC-PUFA in fish tissues, particularly DHA, irrespective of the genotype, as a result of the dietary inclusion of the DHA-rich microalgal oil. Neither genetic selection nor the use of novel raw materials affected fillet proximate composition and consequently, sea bream fillet quality in terms of texture and sensorial perception of consumers. Overall, the results reaffirm the positive effects of selective breeding programs in improving sea bream key productive indicators, as well as support the use of novel dietary formulations, using insect meal from H. illucens, single-cell protein from M. capsulatus as partial replacers of FM in diets for gilthead sea bream (33 and 66% of replacement, respectively), and a blend of DHA-rich microalgal and poultry oils as total replacer of FO.