Lactose hydrolyzed milk powder has low stability at high temperatures or humidity levels, which results in storage technological problems. The molecular structure has been evaluated for powders submitted to accelerated aging (60 °C for 8 h and 24 h) to understand how lactose hydrolysis induces these issues over time. The powders have been evaluated for particle morphology, molecular structures, and rehydration time. The data show that accelerates aging, at the molecular scale, first promotes glycation and a partial unfolding of proteins. In a second time, the same treatment does increase the number of protein-protein covalent links, however, the amount of such protein-protein links is relatively small and it does not completely explain the observed solubility decrease. Instead, the present results indicate that the loss in solubility is rather a consequence of protein glycation which promotes molecular disorder and the subsequence formation of non-native interactions between casein micelles.