The number of aerobic mesophilic bacteria in milk is one of the indicators of the hygienic quality of milk. The aim of this work was to determine such aerobic mesophilic bacteria and their number in raw unpreserved milk and milk preserved with sodium azide. In 40 collected samples, the total number of aerobic mesophilic bacteria was determined using the classical method of counting colonies on a nutrient medium according to the international standard HRN EN ISO 4833-1:2013. The results showed a trend of decreasing the number of grown colonies in milk preserved with sodium azide. MALDI-TOF mass spectrometry also successfully identified 392 bacterial colonies in raw unpreserved milk samples and 330 colonies in preserved milk samples. Of these, 30 genera and 54 bacterial species were identified in the raw unpreserved milk samples, while 27 genera and 41 bacterial species were identified in the preserved samples. By using a collective approach, the present study provided a more detailed insight into milk’s hygienic quality and the presence of certain species before and after the preservation with sodium azide.