Membrane fractionation of cheese whey produces whey protein concentrates and isolates. Its by-product is whey permeate, i.e., a dry residue of lactose and minerals. Permeate possesses high biological (30,000-50,000 mg/L O2) and chemical (60,000-80,000 mg/L O2) oxygen demand. As a result, whey permeate is a potential environmental hazard and cannot be discharged into the sewer as wastewater. Food scientists are looking for a safe and cost-effective method to process whey permeate into value-added products. In this study, whey permeate served as a raw material for a new mixed-fermentation beverage with encapsulated yeast. Some whey permeate samples were fermented with 6.5 × 104 CFU/g of Kluyveromyces marxianus suspense while others were fermented with its encapsulated suspension. The lactose utilization proved to be more intense in the experimental samples with encapsulated yeast. The same samples revealed no presence of yeast during the first 48 h of fermentation. The amount of yeast reached 1.1 × 102 CFU/g after 72 h of fermentation whereas the control sample demonstrated 6.1 × 106 CFU/g. The method of retaining yeast cells in alginate microcapsules prevented it from entering the nutrient medium and growing. The process did not interfere with the lactose utilization and metabolite formation.