Western diets are dominated by the consumption of chemically modified foods, characterized by a deficiency of n-3 polyunsaturated fatty acids (PUFAs). Lack of n-3 PUFAs is also present in livestock feed, which negatively affects livestock health, including immune response, and results in a low content of n-3 PUFAs in animal products. The goal of this experiment was to study the effect of the addition of feed containing PUFAs produced by the fungus Mortierella alpina on immune parameters (IgA, MUC-2, IGF-2, phagocytoses and selected lymphocyte subsets) and the composition of the intestinal microbiota of hens and egg fatty acids profile. Hens were divided into groups (control, F10—supplemented with 10% of fermented feed, F15—supplemented with 15% of fermented feed). The relative expression of all genes was markedly upregulated, mainly in the F15 group. Likewise, in F15, a significant increase in both phagocytes engulfing capacity and the level of oxidative burst was observed. Neither CD T cell subpopulations nor the CD4/CD8 ratio were significantly affected. A significant increase in small intestinal enterobacteria was observed in the F15. The fatty acid profile of eggs in both experimental groups showed an increased proportion of n-3 PUFAs and decreased n-6/n-3 PUFAs ratio. The results of this work show that the addition of 15% omega-3 acids enriched fermented feed positively affected the immune response of laying hens and improved the fatty acid composition of eggs.