The research was aimed at studying the combined effect of micro- and ultrafiltration technological parameters for justification of rational modes in the production of whey protein isolate. The process flow of whey protein isolate production was determined. It includes whey purification from casein dust and fat, pasteurization, ultrafiltration, microfiltration, ultrafiltration (combined with diafiltration), spray drying. Concentration was carried out from a dry matter mass fraction of 5.4-5.6% to 11.3-12.6% (protein concentration factor is 6.5-13). Microfiltration of the resulting retentate was used to maximize disposal of milk fat. The process was carried out using ceramic membranes (pore size from 0.14 pm to 1.4 pm). Their protein retention capacity was 0.2-0.4%, fat retention capacity was 64.6-76.2%. Rational microfiltration modes were selected. They are inlet pressure 0.15-0.2 MPa and temperature 10-15 °C. The microfiltration permeate was treated via repeated ultrafiltration combining it with diafiltration. It was possible to achieve the protein content in dry matter of the product not more than 87% using diafiltration with half the volume of water. However, it does not meet the requirements for the isolate. Increasing the amount of water for diafiltration caused a rise in the protein content in dry matter of the concentrate. The protein mass fraction in the whey protein isolate before drying was at least 17%. The whey protein isolate powder was characterized by the high protein content (93% in terms of SNF), quality and safety indicators met the requirements of regulatory documentation.