The intestinal microbiota plays an important role in the signalling between the gut and the liver. Intestinal bacteria produce short-chain fatty acids and other signalling molecules that affect internal communication. Changes in the composition of the gut microbiota can lead to alternations in this communication, which may ultimately lead to modifications in gene expression driven by epigenetic mechanisms. This study aimed to determine the effect of early microbiome modifications by bioactive substances delivered in ovo on changes in the relative abundance of bacteria in the intestinal contents and the level of expression and methylation of hepatic genes. On day 12 of incubation, a probiotic, a prebiotic, and a synbiotic were injected into the eggs of broiler and Green-legged Partridge-like chickens. Samples were collected post-mortem on day 42. Relative bacterial abundance was analysed using qPCR, gene expression analysis by RT-qPCR, and gene methylation using the MS-qPCR method. It was shown that the relative abundance of the analysed bacteria changed in both genotypes. An increase was observed in the number of Lactobacillus and Bifidobacterium, and a decrease in the number of Escherichia coli in the Polish native breed. A significant increase was demonstrated in DNA methylation of the spleen associated tyrosine kinase gene (SYK) after prebiotic administration in both groups, and the nuclear receptor subfamily 4 group A member 3 gene (NR4A3) in broiler chickens after administration of the synbiotic. Changes in gene methylation correlated with alterations in gene expression. Early stimulation of the gut microbiota at the embryonic stage led to changes in the intestinal microbial profile in adults.