The production of cream cheese, curd, high-protein yogurt, or caseinate results in large amounts of acid whey as a by-product. So far acid whey is often disposed as animal feed or organic fertilizer. However, these approaches ignore the valorization potential that arises from the unique composition of the whey protein fraction. Whey contains the biofunctional proteins lactoferrin and immunoglobulin G, which possess immune-supporting, antibacterial, antiviral, and numerous further health-promoting functions. However, the concentration of these proteins in bovine milk or whey is below a physiologically relevant level. Based on literature research we specified a daily intake of 200 mg lactoferrin as the minimal functional dose. By means of cross-flow ultrafiltration, an attempt was made to increase the concentration of biofunctional proteins. Therefore, a membrane for the selective retention of lactoferrin and immunoglobulin G was identified, and the process parameters were optimized. Finally, a concentration experiment was conducted, whereby the concentration of biofunctional proteins was increased up to factor 30. The biofunctionality was assessed in a microbiological assay. Surprisingly, the antimicrobial growth inhibition of the produced concentrate was even higher than in pure lactoferrin. The presented approach offers a strategy to convert an abundant but underutilized by-product into valuable products for human nutrition.