This study investigated the impact of Korean rice wine (makgeolli) consumption on human gut microbiota and compared it with that of other alcoholic beverages, including soju (Korean spirit), beer, and red wine. A randomized, cross-over trial design was employed, and fecal samples were collected from 18 healthy adults before and after the consumption of rice wine or control liquor. Microbiota of each fecal sample was analyzed targeting V3–V4 region, utilizing MiSeq system and QIIME2 analysis. Significant alterations in the relative abundance of the Actinobacteria and certain genera were observed after rice wine intervention. Additionally, rice wine consumption induced distinct alterations in the gut microbiota compared with other liquor consumptions. The relative abundance of lactic acid bacteria in the gut microbiota varied among the participants, with an elevated detection frequency of Enterococcus and Lactobacillus genera observed following rice wine consumption. In summary, this study provides the first comprehensive insight into the unique effect of rice wine consumption on the human gut microbiota, distinguishing it from other liquors. Display omitted •This is the first exploration of rice wine intake impact on human gut microbiota.•Rice wine consumption led the alteration of certain human gut microbial genera.•The human gut microbiota shift upon rice wine intake differed from other liquors.•Impact of rice wine consumption varied based on the enterotype of each participant.•Rice wine intake led increased detection frequency and abundance of Lactobacillus.