Liquid milk protein concentrate with different beneficial values was prepared by membrane filtration and enzymatic modification of proteins in a sequential way. In the first step, milk protein concentrate was produced from ultra-heat-treated skimmed milk by removing milk serum as permeate. A tubular ceramic-made membrane with filtration area 5 × 10−3 m2 and pore size 5 nm, placed in a cross-flow membrane house, was adopted. Superior operational strategy in filtration process was herein: trans-membrane pressure 3 bar, retention flow rate 100 L·h−1, and implementation of a static turbulence promoter within the tubular membrane. Milk with concentrated proteins from retentate side was treated with the different concentrations of trypsin, ranging from 0.008−0.064 g·L−1 in individual batch-mode operations at temperature 40 °C for 10 min. Subsequently, inactivation of trypsin in reaction was done at a temperature of 70 °C for 30 min of incubation. Antioxidant capacity in enzyme-treated liquid milk protein concentrate was measured with the Ferric reducing ability of plasma assay. The reduction of angiotensin converting enzyme activity by enzyme-treated liquid milk protein concentrate was measured with substrate (Abz-FRK(Dnp)-P) and recombinant angiotensin converting enzyme. The antibacterial activity of enzyme-treated liquid milk protein concentrate towards Bacillus cereus and Staphylococcus aureus was tested. Antioxidant capacity, anti-angiotensin converting enzyme activity, and antibacterial activity were increased with the increase of trypsin concentration in proteolytic reaction. Immune-reactive proteins in enzyme-treated liquid milk protein concentrate were identified with clinically proved milk positive pooled human serum and peroxidase-labelled anti-human Immunoglobulin E. The reduction of allergenicity in milk protein concentrate was enzyme dose-dependent.