Lactose hydrolyzed milk powder production remains a challenge for the dairy industry because of specific technological problems, such as stickiness and caking during drying. The molecular mechanisms that lead to these problems are poorly understood. The aim of this study was to provide a better understanding of how galactose and glucose affect the organization and physicochemical behavior of milk powder molecules. In order to do so, we analyzed the organization and dynamics of lactose hydrolyzed milk powder particles after lactose hydrolyzed milk had been processed under anti-caking conditions. In general, the structure of the lactose hydrolyzed milk powder sample was characterized by a greater number of monosaccharides around proteins compared to those found in the lactose of a traditional milk powder sample. This difference can be explained by a combination of greater repulsive interactions between proteins as well a stronger attractive interaction between proteins and monosaccharides. Our data indicated that this difference in the molecular organization impacted milk powder’s hydration kinetics.