Two pasteurization steps are often used in the preparation of whey protein concentrate (WPC) before evaporation into a dry product. The Pasteurized Milk Ordinance (PMO) in the United States requires that raw bovine milk be pasteurized using a process that meets minimum heat treatment requirements to achieve reductions in pertinent microorganisms. In addition, WPC produced from USDA-approved plants must comply with CFR Subpart B §58.809, which dictates that all fluid whey used in the manufacture of dry whey products shall be pasteurized before being condensed. These heat treatments are effective at inactivating the most thermally resistant bacterium, such as Coxiella burnetii; however, they can also alter milk proteins-inducing denaturation, aggregation and reduced bioactivity. Though the impact of thermal treatments on whey proteins has been examined, the specific influence of 2 high-temperature-short-time (HTST) pasteurization steps on the retention of proteins in WPC remains unknown. This study aimed to investigate the effect of commercial-scale HTST pasteurization of both raw milk and the resulting sweet whey on the products' overall protein profile. Three distinct batches of raw milk (RM) and corresponding pasteurized milk (PM), the resulting whey (RW) and pasteurized whey (PW) produced at commercial scale were analyzed. Assessments of denaturation were conducted through solubility testing at pH 4.6 and hydrophobicity evaluation via anilinonaphthalene-1-sulfonic acid assay (ANS). Additionally, enzyme-linked immunosorbent assay (ELISA), PAGE (PAGE) and liquid chromatography tandem mass spectroscopy (LC-MS/MS) were employed to compare the retention of key bioactive proteins before and after each HTST pasteurization step. The percentage of soluble whey protein decreased from RM to PM and from RW to PW, but no significant differences were observed via hydrophobicity assay. ELISA revealed a significant reduction in key bioactive proteins, such as lactoferrin, immunoglobulin A and immunoglobulin M, but not immunoglobulin G, after HTST pasteurization of RM and RW. PAGE and LC-MS/MS revealed a significant decrease in the retention of lactoferrin and key milk fat globular membrane proteins, such as xanthine dehydrogenase oxidase/xanthine oxidase, lactadherin and fatty acid binding protein. Additionally, xanthine oxidase activity was significantly reduced after HTST pasteurization of milk and whey. This research helps to identify the limitations of the current processing techniques used in the dairy industry and could lead to innovation in improving the retention of bioactive proteins.