Whole milk powder (WMP) is a universal raw material component that can overcome the problem of seasonality of raw milk. It can be used to provide high-nutritional products to remote areas experiencing a raw milk shortage. Its long shelf life depends on the conditions of storage and transportation, which are recommended to be carried out in a range from 0 to 10°C. At higher temperatures, the quality of WMP deteriorates because of a substantial increase in the degradation of fat and protein fractions. A range of low negative temperatures for storage have not been systematically investigated. Previous studies have shown that freezing WMP results in protein denaturation, crystallization of lactose, and extraction of free fat, all of which reduce the quality characteristics of the product, including deterioration of solubility, quick rancidification, and microbiological changes. However, these previous studies did not simulate the possible situations of transportation and storage of milk powder at low negative temperatures that occur in practice. Given the volume of transportation, distances and climatic characteristics of transportation routes play an important role in WMP preservation. In this study, we simulated storage and transport of WMP at -20°C. The samples were periodically thawed to 10 and 20°C and examined for physicochemical, functional-technological, thermodynamic, microbiological, and organoleptic parameters. Based on our results, storage of WMP at -20°C for 40 d did not have a significant effect on its qualitative characteristics. We observed some compaction of product structure and clustering or clumping, which was reversible by slight mechanical impact. Artificial contamination of the packaging surface with yeast and molds, followed by thawing of the samples, indicated the absence of the contaminants, which was explained by possible redistribution of moisture in the system.