This study was carried out on the effect of different amounts of whey on the kefir production process and the bacterial microbiota of the beverages. Fermentation was carried out by mixing commercial kefir grains with cow, sheep, and goat milk with their whey at concentrations of 0% (control group), 25%, 50%, and 75%. The bacterial microbiota in the produced beverages and the relative abundances of seven microorganisms (Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus delbrueckii, Lactococcus lactis, Streptococcus thermophilus, Leuconostoc mesenteroides, and acetic acid bacteria) were determined using metagenomic analysis targeting the V3-V4 region of 16 S rRNA gene, and quantitative polymerase chain reaction (qPCR), respectively. Lactococcus lactis and Leuconostoc mesenteroides were detected in higher abundance in whey-containing goat samples. While Lactobacillus was dominant in the cow milk samples containing 0%, 25%, and 50% whey, Enterococcus was dominant in the samples containing 75% whey. In sheep milk samples, Lactobacillus was dominant in samples with 75% and 50% whey, Lactococcus was dominant in samples with 25% whey, and Enterococcus was dominant in samples with no (0%) whey. Lactobacillus was dominant in all goat milk samples. In conclusion, high levels of lactic acid bacteria were shown to preserve their viability in the experimentally produced beverages with the addition of whey at different concentrations, and the whey could be used to produce kefir.