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To lower the risk of obesity, diabetes, and other related diseases, the WHO recommends that consumers reduce their consumption of sugars. Here, we propose a microbiological method to reduce the sugar content in red beet juice, while incurring only slight losses in the betalain content and maintaining the correct proportion of the other beet juice components. Several yeast strains with different metabolic activities were investigated for their ability to reduce the sugar content in red beet juice, which resulted in a decrease in the extract level corresponding to sugar content from 49.7% to 58.2%. This strategy was found to have the additional advantage of increasing the chemical and microbial stability of the red beet juice. Only slight losses of betalain pigments were noted, to final concentrations of 5.11% w/v and 2.56% w/v for the red and yellow fractions, respectively.