Low-frequency ultrasound (20 kHz) was applied to model casein (CF) and whey protein (WF) milk systems with varying fat contents of 2%, 4%, and 6% (w/w) under different energy densities from 9.54 to 190.8 J mL−1. The study used Fourier transform mid-infrared spectrometry (FT-MIR) to analyse the modification of milk proteins and fat. The results showed that the fat content and sonication time influenced the intensities of fatty chains and ester groups which are assigned to triacylglycerols and lipid-protein complexes for both CF and WF systems. Acoustic cavitation induced structural changes of proteins due to denaturation/aggregation and disruption of milk fat globules/fat clusters led to new protein–protein and protein-lipid interactions.