The use of low-concentration factor ultrafiltered (LCF-UF) milk for cheesemaking has become popular in recent years. Research on using LCF-UF milk to make low-moisture part-skim (LMPS) Mozzarella manufacture is limited due to concerns about the negative impact of the higher casein content on functional properties, such as melt and stretch. Pre-acidification (PA) (reflects acid added to milk before the addition of the starter culture) has been used in low-fat and nonfat Mozzarella cheeses to lower calcium levels and improve their texture and melting properties. We explored the use of PA to reduce the insoluble calcium content of cheese (calcium that is a crosslinking material for the casein proteins) and its impact on the functionality of LMPS Mozzarella made from high casein (4.2%) milk. Seven vats of LMPS Mozzarella, with a control (no PA), 2 pH values for PA (6.40 and 6.00) and 3 different acidification methods (use of acetic, citric, or carbonic acid from carbon dioxide) were evaluated for their impact on solubilization of colloidal calcium phosphate during LMPS manufacture. Composition, proteolysis, microstructural and functional changes in the LMPS cheeses were monitored during 90 d of refrigerated storage. All cheeses had similar composition except for the cheese made with milk PA with carbonic acid, which had a lower fat-in-dry matter probably due to foaming observed in this sample during the gas sparging. The cheese made with milk PA with citric acid to pH 6.00 had the lowest amount of total and insoluble calcium compared with other cheeses at all steps during cheese manufacture and storage, likely due to the calcium chelating ability of citric acid. The cheese that was made with milk PA with citric acid to pH 6.40 had a trend of slightly lower (not significant) total and insoluble calcium during cheese manufacture compared with other cheeses that were made with milk PA to pH 6.40. The pH value in all the cheeses remained similar throughout 90 d of storage, whereas the cheese that was made with milk PA with citric acid to pH 6.00 had the lowest pH values during storage. Treatment significantly (P < 0.05) impacted instrumental hardness, the maximum loss tangent during heating, the melting temperature and the storage modulus values measured at 70°C. Proteolysis was not impacted by treatment suggesting that typical aging should occur. Cheese that was PA with citric acid to pH 6.00 initially had lower maximum loss tangent values and higher hardness, possibly due to the lower pH value of this cheese. The performance of cheeses on pizza was assessed using Sensory Spectrum® method and quantitative descriptive analysis. The PA of cheese milk with citric acid helped to reduce the insoluble Ca level and at 30 and 90 d of storage, these cheeses had lower first chew hardness, lower chewiness, and lower strand thickness values compared with other cheeses. The use of PA could help improve the functionality of LMPS Mozzarella made from milk high in casein with citric acid being the most efficient in dissolving the insoluble calcium from casein.