Commercial kefir was recently found to be effective in curing recurrent Clostridioides difficile infection when consumed alongside antibiotic treatment. However, kefir products have limited acceptance among Western consumers due to their characteristic flavor and texture. Plain, unsweetened commercial kefir with 1% milkfat was subjected to vacuum evaporation and freeze-drying processes to assess the effect on volatile organic compound concentration, sensory quality, and microbial viability. Vacuum evaporation and freeze-drying both significantly decreased the concentration of 26 out of 27 volatiles in the kefir (p < 0.05), by an average of 61%. Vacuum evaporation exhibited an apparent greater reduction than freeze-drying in the concentrations of the ketones and aldehydes, while freeze-drying showed a more noticeable reduction in the concentrations of the acids, alcohols, and esters. While lowering the concentration of volatiles did not significantly improve the average consumer acceptance of commercial kefir, both treatments showed differences in the range of acceptability responses. Both treatments also produced a small but significant reduction in the concentrations of Lactobacillus and Lactococcus species present.