Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are essential fatty acids (EFA) vital for Atlantic salmon health, growth performance, and product quality. Yet, DHA and especially EPA are in short supply as ingredients for aquafeeds. Whilst the role of EFA in salmonid nutrition has been well studied, clear guidelines for aquaculture nutrition practitioners are still missing. This article addresses this gap by testing different EPA:DHA ratios (0.15, 0.55, and 0.98) when these two EFA represent at least 10% of the total pool of fatty acids in aquafeeds. Grow-out trials revealed no differences in zootechnical performance between fish fed the different diets during the initial eight weeks before vaccination challenge, nor on the subsequent three weeks post-vaccination for fish truly vaccinated or sham vaccinated (used as control groups for each of the three diets tested). Nonetheless, the FCR of vaccinated fish was significantly higher than sham vaccinated conspecifics, but diet yielded no significant effect. The expression of most genes screened (e.g., Elongation Factor 1α (Elf-1α), Interleukin 10 (IL10), Interleukin 8 (IL8), Tumor Necrosis Factor (TNFα)) was not significantly affected by vaccination or diet, while Viperine and Mx genes were upregulated in sham vaccinated fish fed the experimental diet with an EPA:DHA ratio of 0.55. The fatty acid composition of head kidney was affected by diet, namely EPA, but not DHA. The fatty acid profile of white muscle was also significantly affected by diet, with contrasting results for EPA and DHA; EPA content was higher for fish fed diets with higher EPA:DHA ratios and DHA levels were significantly higher (peaking at 16% of the total pool of fatty acids) when fish were provided with the diet featuring the lowest EPA:DHA ratio (0.15). Interestingly, fish fed the diet with the highest EPA:DHA ratio showed a lower number of wounded fish at the end of the grow-out period post-vaccination. Despite the reduction was not statistically significant, given the severe impact of wounded fish on salmon farming productivity, our results indicate that the partial replacement of fish oil with algal oil in salmon feed contributed to achieving a balanced EPA:DHA ratio, an adequate profile of Omega-3 long chain polyunsaturated fatty acids and improved the overall health and welfare of fish. This approach creates the opportunity to increase the productivity of fish farming operations and foster a more sustainable growth of the aquaculture industry.