The most widely used whey protein ingredient in an infant formula (IF) is the whey protein concentrate (WPC). The processing steps used in the manufacturing of both a powdered IF and a WPC introduce protein modifications that may decrease the nutritional quality. A gently processed whey protein ingredient (serum protein concentrate; SPC) was manufactured and used for the production of a powdered IF. The SPC and the SPC-based IF were compared to the WPC and the powdered WPC-based IF. Structural protein modifications were evaluated, and Maillard reaction products, covering furosine, alpha-dicarbonyls, furans, and advanced glycation end products, were quantified in the IFs and their protein ingredients. IF processing was responsible for higher levels of protein modifications compared to the levels observed in the SPC and WPC. Furosine levels and aggregation were most pronounced in the WPC, but the SPC contained a high level of methylglyoxal, revealing that other processing factors should be considered in addition to thermal processing.