This study determined changes in the live lactic microflora of cow and goat milk kefirs, traditionally produced using kefir grain and freeze stored for 30 days, using high-throughput sequencing. In kefir grains, 71.29% Lactococcus, 16.27% Enterococcus, and 12.3% Serratia were found in the M17 agar, and 69.93% Lacticaseibacillus and 24.54% Lactobacillus were found in MRS agar. In the M17 agar of cow milk kefir, 78.26% Lactococcus was found on day 0, and this rate was 91.68%, 87.98%, and 88.14%, on the 7th, 14th, and 30th days, respectively. As for goat milk kefir, Lactococcus levels were 82.98%, 93.28%, 87.77%, and 84.92%, respectively. On the MRS agar in cow milk kefirs, Lacticaseibacillus levels were found as 56.98%, 61.21%, 87.54%, and 75.50%, on days 0, 7, 14, and 30 of storage, respectively, while the rates were 48.95%, 77.02%, 87.85%, and 83.38% for goat milk kefirs, respectively. As a result, although kefir beverages frozen at −25°C contain sufficient levels of Lactobacillus and Lactococcus, it has been determined that the genus Serratia, which is one of the main spoilage factors in dairy products, is also increasing. Novelty impact statement: In this study, the changes in the living lactic microflora during the frozen storage of traditional kefir beverages, whose production is increasing, were determined by high-throughput sequencing. It is thought that it is important to determine the effect of the freezing process on the viability of lactic acid bacteria, which are thought to have probiotic properties, for the long-term storage of these beverages. However, while lactic acid bacteria maintain their viability, it should be taken into account that microorganisms that are resistant to freeze conditions and cause spoilage can also develop.