Gastrointestinal infectious diseases accompany the growth of animal and poultry farming: as the livestock population increases, its high concentration on farms raises the level of mortality and rejection, thus reducing the overall safety and productivity. Probiotics and prebiotics used as feed additives may be an effective preventive measure. The article describes a sustainable and environmentally friendly method for obtaining prebiotics of pectin oligosaccharides by hydrolyzing apple pomace pectin in whey with Saccharomyces cerevisiae to produce bifidogenic animal feed. The 5:1 ratio of whey and apple pomace increased the yeast biomass by 56.3% after 24 h of fermentation and introducing 0.3% yeast by weight. The pectin hydrolysis products triggered an intensive growth of the substrate. The hydrolysis products contained 32% oligosaccharides of average molecular weight. The enzymatic hydrolysis of whey-apple mixes with a β-galactosidase preparation by deep cultivation of Bacillus licheniformis prevented the negative effect of serum lactose consumption, as well as increased the yield of yeast biomass. The optimal hydrolysis parameters were pH 6.0, 25 °C, 0.04% enzyme, and 6 h. The technological process included the following stages. The raw materials were prepared as a whey-vegetable mix (5:1), which was gradually heated to 65 °C. After cooling down to 22-25 °C, dry Saccharomyces cerevisiae provided fermentation and deoxidation. After introducing lactase enzyme and final thermal treatment, the finished feed additive contained 10% solids, 3.5% nitrogenous substances, 0.6% pectin, 0.3% pectin oligosaccharides, and 0.2% residual lactose, as well as vitamins and minerals.