The effectiveness of microfiltration (MF), alone or combined with high temperature short time (HTST) pasteurisation, ultraviolet-C (UV-C), and ultrasonication (US) in improving the microbial and nutritional quality of skim milk was evaluated in comparison with commercial ultra-pasteurisation (UP). Compared with untreated skim milk, MF combined with UV-C and US retained more bioactive proteins, which made these techniques superior to MF combined with HTST. Almost no bioactive proteins survived after UP. MF alone reduced the bacterial load by 2.5 log; however, MF combined with HTST (MH), UV-C (MUV), or US (MUS) can reduce the bacterial load to an undetectable level and extend the microbial shelf-life of skim milk to 40 days. In addition, MUV and MUS did not induce significant protein oxidation. Even though the skim milk after MUV or MUS showed only minor microbial growth, the shelf-life was limited by proteolysis through plasmin activity.