Ultrasonication, like common shear homogenization, can reduce the milk fat globule size and may change the milk fat globule membrane (MFGM). This work compared the effect of ultrasonication to equivalent shear homogenization on MFGM proteins and lipid-derived volatile components. Results showed that treating milk with ultrasound at 35 kJ/L would realize a similar size distribution of the milk fat globules as shear-homogenization at 20 MPa. Proteomics analysis revealed that in total 192 MFGM proteins were identified and quantified and a number of these proteins were lost after both treatments; however, more MFGM proteins remained after ultrasonication than after shear-homogenization. SDS-PAGE results showed that milk plasma proteins, and especially caseins, were absorbed on the milk fat globules after both treatments. In addition, the amount of the volatile free fatty acids increased after both treatments. Industrial relevance: Ultrasonication, as an innovative food processing technology, in comparison to traditional homogenization, was shown to equally efficiently decrease the MFG size, but lead to less damage to native MFGM proteins, which may be due to its longer homogenization time window. These results increased knowledge on the biochemical changes of milk fat globules after their size reduction and showed that ultrasonication could be used as a novel approach to improve dairy product quality.