Thermal processing of foods results in proteins undergoing conformational changes, aggregation, and chemical modification notably with sugars via the Maillard reaction. This can impact their functional, nutritional, and allergenic properties. Native size-exclusion chromatography with online electrospray mass spectrometry (SEC-ESI-MS) was used to characterize processing-induced changes in milk proteins in a range of milk products. Milk products could be readily grouped into either pasteurized liquid milks, heavily processed milks, or milk powders by SEC behavior, particularly by aggregation of whey proteins by thermal processing. Maillard modification of all major milk proteins by lactose was observed by MS and was primarily present in milk powders. The method developed is a rapid tool for fingerprinting the processing history of milk and has potential as a quality control method for food ingredient manufacture. The method described here can profile milk protein oligomeric state, aggregation, and Maillard modification in a single shot, rapid analysis.