Reduced fish oil (FO) inclusion in salmon feeds has lowered dietary EPA (20:5n-3) and DHA (22:6n-3), highlighting the need to better understand how their levels and relative ratios affect fish performance, health, and fillet quality. This study used three diets in triplicate commercial-scale cages in seawater (Oct 2022 – Jan 2024) under challenging farming conditions in Arctic Finnmark, Norway. Diets contained 7.5 % or 10 % EPA+DHA of total fatty acids (FA), supplied by FO or equal parts FO and DHA-rich algal oil (AO): FO7.5 (EPA:DHA 0.6), FO10 (1.7), and FO5AO5 (0.3). Final body weight reached 4.8 kg in FO7.5 and FO5AO5 and was 0.6 kg lower in FO10 (P = 0.08). FO10 showed lowest mortality (6.5 % vs. 9 %; P = 0.008), mainly due to fewer and smaller skin wounds (r = 0.91, P < 0.0001), but also less heart-related losses (P < 0.01). Handling-related mortality was higher in FO7.5 than FO5AO5 (P = 0.03), but not FO10 (P = 0.11). Reduced wounds in FO10 increased harvest superior-grades (P < 0.004), associated with higher EPA levels (r = −0.76, P < 0.03), but not DHA. In vitro exposure of scale explants to Moritella viscosa linked FO10 to improved skin health through enhanced wound repair, immune activation, and metabolic regulation. FO10 fish had larger hearts, smaller livers, and lower slaughter yield, while FO7.5 had highest distal intestinal mucosal atrophy at harvest (P = 0.04), higher fillet fat than FO10 (P = 0.03), and higher skin fat than FO5AO5 (P = 0.02). FO10 and FO5AO5 had highest EPA+DHA fillet levels, with FO10 yielding highest EPA and FO5AO5 highest DHA. Dietary FA’s significantly regulated lipid partitioning and storage patterns among tissues. Both FO10 and FO5AO5 had reduced fillet gaping, while FO5AO5 fillets were paler and softer. Overall, EPA-rich diets improved resilience under infectious stress, enhancing wound repair, heart health, survival and product quality. These benefits occurred alongside lower slaughter yield and seemingly lower growth of FO10, highlighting trade-offs in diet evaluation where growth, health, and product quality may diverge.