A cheese‐making process was developed which utilizes concentration factor (CF) 8, pH 6.0 skim milk microfiltration (MF) retentate to produce low‐moisture, part‐skim (LMPS) Mozzarella cheese. The compositional and proteolytic effects of different levels of rennet concentration, coagulation temperature, and post‐coagulation curd cutting time were evaluated, with rennet concentration having the strongest influence. A post‐coagulation curd cutting time of 15–20 min was found to normalize the extent of κ‐casein hydrolysis during coagulation of concentrated MF retentate. Optimal cheese manufacturing parameters were determined to be 80–100 μL rennet kg–1 MF cheesemilk, coagulation temperature of 32–36 °C, and post‐coagulation curd cutting time of 15 min. As compared with ultrafiltration (UF) retentate cheese manufacture, cheese made from MF retentates has potential for improved textural and functional qualities, along with recovery of highly functional whey proteins (WP) from permeate.