Kefir is a fermented beverage produced through the activity of its grains, which is constituted by lactic acid and acetic acid bacteria and yeasts. We studied the bacterial succession during multiple fermentation of Argentinian kefir in brown sugar, purified molasses or high-test molasses, using 16S high-throughput sequencing. Firmicutes was dominant (up to 98% of total population) in grains and beverages made from various sugar substrates, except in high-test molasses beverage, which was dominated by Proteobacteria (up to 78% of total population). Major bacterial species in Firmicutes were Liquorilactobacillus nagelii, Lentilactobacillus hilgardii/diolivorans and Lacticaseibacillus casei/paracasei, which are active in lactic acid fermentation. Proteobacteria comprised Acetobacter lovaniensis and Gluconobacter oxydans/roseus as major species, which are presumably responsible for the acetic acid formation in sugary kefir beverages. Bacteria differ in abundance depending on the sugar type, as revealed by the competitive dominances between L. nagelii and A. loveniensis. Purified molasses led to scarce acetic acid bacteria during fermentation, indicating that it is not a suitable substrate for their growth. Our results suggest that acetic acid (and/or ethanol) in sugary kefir modulates the succession and dominance of specific lactic acid bacteria. This study will provide valuable information for designing more sophisticated non-dairy fermented beverages with stable microbial properties.