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Comparative metatranscriptomics of the bacterial and yeast communities of two milk kefir beverages (MKAA1 and MKAA2) was carried out. They were obtained by fermentation with two different frozen stocks of the kefir grain CIDCA AGK1, differing in rheological features and production of organic acids. We hypothesised that the differences in their physicochemical and rheological properties might be due to the microbial activity in each product. The dominance of lactic acid bacteria, yeast, and a marginal amount of acetic acid bacteria characterised the microbiome. The bacterial families <i>Lactobacillaceae</i> and <i>Streptococcaceae</i> accounted for almost all of the bacterial gene transcripts, with <i>Lactobacillus helveticus</i>, <i>L. kefiranofaciens</i>, <i>L. gallinarum</i>, and <i>Lactococcus lactis</i> being most frequent in the microbiome of the MKAA1 beverage and <i>L. kefiranofaciens</i>, <i>Lc. Lactis</i>, and <i>Leuconostoc mesenteroides</i> being the most prevalent in MKAA2. <i>Dipodascaceae</i> and <i>Saccharomycetaceae</i> were the leading yeast families, represented by <i>Yarrowia lipolytica</i>, <i>Saccharomyces unisporus,</i> and <i>Kluyveromyces marxianus</i>. MKAA1 and MKAA2 shared >75% KEGG Ortologs (KOs) in their bacteria and yeast libraries. The considerable decreases in total expressed genes (KEGG Ortologs) assigned to <i>Lactobacillus helveticus</i> and <i>L. gallinarum</i> might be related to the variations in the rheological features of the beverages, probably by compromising the interrelations with <i>L. kefiranofaciens</i>, which might explain the variations in the rheological features of the beverages.