Beige adipocytes are transiently induced during early postnatal period in mice. Previous studies have suggested that, unlike in adults, the induction is independent of the sympathetic nerve activity; however, the mechanism is yet unknown. Here, we showed that beige adipocytes are induced during the preweaning period in association with the formation of microbiota in mice. Alteration of gut microbiota composition in preweaning mice by maternal treatment with antibiotics or high-fat diet feeding substantially suppressed WAT browning. The suppression was also found in pups transplanted cecal microbiota from pups of high-fat diet-fed dams. These treatments reduced the hepatic expression of genes involved in bile acid synthesis and the serum bile acids level. The abundance of Porphyromonadaceae and Ruminococcaceae in microbiota showed a positive and negative correlation with the induction of beige adipocytes, respectively. This finding may provide comprehensive understanding of the association between gut microbiota and adipose tissue development in the neonatal period.