Reconstituted skim milk was subjected to heat treatment at 85 °C for 20 min or high pressure processing (HPP) at 400 or 600 MPa for 15 min with or without subsequent high intensity ultrasound (US) at 68 kHz, 500 W for 15 min at 30 °C. Untreated and treated samples were analyzed for particle size distribution, zeta potential, surface hydrophobicity, and concentration of total and surface sulfhydryl groups in addition to Native- and SDS-PAGE of serum phase upon ultracentrifugation and pH adjustment. Preceding heat- and HPP altered the impact of the subsequent US treatment, demonstrating process- and intensity-dependent exposure and burial of surface reactive sites on milk proteins respectively. US following HPP promoted sedimentation of HPP-dispersed serum casein fractions, while US following heat was directed mainly at the whey proteins originally bound to the micelles. The primary US effect on the untreated and treated milk proteins was at the molecular level.