Recent reports suggest that obesity is caused by dysbiosis of gut microbiota and that it could be prevented or treated through improvement in the composition and diversity of gut microbiota. In this study, high-fat diet (HFD)-induced obese mice were orally administered with Lactobacillus plantarum K50 (K50) isolated from kimchi and Lactobacillus rhamnosus GG (LGG) as a positive control for 12 weeks. Body weight and weights of epididymal, mesenteric, and subcutaneous adipose tissues and the liver were significantly reduced in K50-treated HFD-fed mice compared with HFD-fed mice. The serum triglyceride level was decreased and high-density lipoprotein cholesterol level was increased in K50-treated HFD-fed mice. The gut microbiota analysis showed that the L. plantarum K50 treatment reduced the Firmicutes/Bacteroidetes ratio and improved the gut microbiota composition. In addition, the level of total short-chain fatty acids (SCFAs) in K50-treated HFD-fed mice was higher than that in HFD-fed mice. A remarkable reduction in the fat content of adipose tissue and liver was also observed in K50-treated HFD-fed mice, accompanied by improvements in gene expression related to lipid metabolism, adipogenesis, and SCFA receptors. K50-treated mice had downregulated expression levels of genes and proteins such as TNF alpha and IL-1 beta. Our findings confirm that L. plantarum K50 could be a good candidate for ameliorating fat accumulation and low-grade inflammation in metabolic tissues through gut microbiota improvement.