Reconstituted skim milk powder (RSMP) was homogenized at different pressures (41–186 MPa), and with up to six passes. The higher the pressure and the more passes employed, the smaller was the average diameter of the casein micelles. Different combinations of heat and pressure treatments were employed: control (C), homogenization at 186 MPa (H), heat (T) at 85 °C for 10 min, homogenization then heat (HT), and heat then homogenization (TH). The effect of homogenization on the decrease in micelle size was found to be H>TH>HT>T=C. The serum phase of homogenized milks (H) showed different protein size exclusion profiles compared with those from other treatments. The ultra-high-pressure homogenization (UHPH) was found to increase the amount of non-sedimentable caseins (κ, αs1 and αs2) in the serum. Electron microscopy showed formation of smaller particles following treatments H, TH, and HT when compared with C. It was concluded that UHPH was capable of modifying the structural properties of casein micelles and that the sequence of treatments was an important factor in determining the nature of the modifications.