The development of sustainable aquaculture relies on replacing marine raw materials like fish meal (FM) and fish oil (FO). Emerging alternatives, such as single-cell proteins and alternative lipids, offer promise. This study explored the effects of partially substituting FM with 10% bacterial protein (Methylococcus capsulatus) and completely replacing FO with a blend of poultry oil (PO) and DHA-rich microalgae oil in European sea bass (Dicentrarchus labrax) of unselected (WT) and selected (HG) genotypes. The results indicated that bacterial protein had no adverse impact on fish growth. The HG group demonstrated better growth and feed conversion due to genetic selection. This study also analysed the dietary and genotype effects on body lipid composition and fatty acid profiles. Notably, the HG fish had lower levels of major fatty acids (EPA, DHA, n-3 FAs, and n-3 LC-PUFAs) in their fillets, but not in their whole-body composition. These differences influenced sensory and qualitative aspects. Electronic sensory analyses (the first e-sensory profiling conducted for genetic purposes in fish) showed more significant differences due to diet in the WT group, with a less variable pattern in the e-tongue score in for the HG group. The volatile profiles showed no significant differences. In summary, combining selected fish genotypes with innovative feeds is a step forward in aquaculture. It maximizes nutrient utilization, enhances fish growth, and improves product quality. This approach becomes increasingly important in scenarios with limited FM/FO availability, promoting sustainability in aquaculture.