Dairy products are relevant in the food industries as functional ingredients for several food products and contribute towards human nutrition in ameliorating certain disorders. In this study, set yogurts were produced from raw milk and processed milk combined with 4% Lacprodan^®PL20 concentration and subjected to two-stage pressure homogenization. The total solids concentration of the mixture was raised to 15% using SMP (skim milk powder). The purpose of this study was to investigate the effect of Lacprodan^®PL20 on the set yogurt quality produced by homogenization-induced pressure and its interaction with milk components. The changes in the physical and chemical attributes of the milk fat globule membrane (MFGM) via destabilization of the membrane significantly affected the physicochemical properties of set yogurts produced from processed or raw milk. There was a slight variation in MFGM-specific proteins detected in the set yogurts. Set yogurt produced from homogenized raw milk (HRM) had a considerably higher water-holding capacity, firmness, and apparent viscosity. The microstructure of HRM was dense and compacted, unlike non-homogenized raw milk (NRM) with large MFGM fragments and pore holes between the matrixes. The inclusion of homogenization showed a remarkable improvement in set yogurt quality, promoting interaction between MFGM components and milk proteins.