The chemical stability of valuable nutrients like the essential amino acid lysine is an important factor regarding the nutritional quality of dairy powders. So far, the stability concepts based on the water activity or on the glass transition temperature are mainly used to predict the stability of dairy powders. However, these concepts often only partly predict the stability of food products. Therefore, the aim of this study was to complement the established stability concepts by the molecular mobility as measured by low resolution 1H NMR to fill this gap. Glass transition and crystallization of lactose were measured by differential scanning calorimetry. The delay of lactose crystallization was a function of the glass transition temperature and could be modeled by the Williams–Landel–Ferry equation. Lactose crystallization kinetics could not be modeled by the Avrami equation which indicates the formation of different crystal forms. The molecular mobility measured by low resolution 1H NMR proved to be a fast and easy to handle method for the characterization of dairy powders. The transversal relaxation time showed a sharp increase above the glass transition temperature and increased further in the crystalline state. However, the crystallization conditions affected the transversal relaxation time in the crystalline state which indicated the formation of different crystal forms in accordance with the observations of the lactose crystallization kinetics. Furthermore, crystallization led to a step increase of the second moment. Hence, low resolution 1H NMR could also be used to analyze the crystalline structure. The extent of lysine loss in three different dairy formulations after a thermal treatment could be explained by taking into account the physical state together with the molecular mobility. Thus, it can be concluded that both the physical state and the molecular mobility are decisive for the chemical stability of dairy powders.