In the grain samples of three malting barley varieties harvested in 2016, and in the malt made from them, we observed microbial changes during storage. Analyses were performed after 0, 3, 6, and 9 months of storage in floor warehouses and silos. We monitored microbial changes based on the quantitative determination of microorganisms using a plate dilution method and qualitative determination of microorganisms, where we identified a particular species of bacteria using the MALDI-TOF MS Biotyper instrument (Bruker Daltonics, Bremen, Germany). Based on the quantitative determination of microorganisms, we found that the total plate counts of microorganisms was higher in malts than in barley grains. The storage period had the greatest impact on the number of coliform bacteria, which gradually increased with the growing months in storage. The number of lactic acid bacteria in barley grains with the growing months in storage and malt produced from them decreased slightly, and the content of the sporulating bacteria in all the samples fluctuated slightly. Differences in the numbers of observed microorganisms were negligible during storage between floor warehouses and silos. In the samples of barleys, the most commonly identified species were Pantoea agglomerans, which was also present in malt samples but did not belong to the dominant species. A diverse species representation appeared in the samples, whereas predominating species belonged to the Enterobacteriaceae family.