The effects of Lactiplantibacillus plantarum 06CC2 (LP06CC2), which was isolated from a Mongolian dairy product, on lipid metabolism and intestinal tight junction-related proteins in Balb/c mice fed a high-fat diet (HFD) were evaluated. The mice were fed the HFD for eight weeks, and the plasma and hepatic lipid parameters, as well as the intestinal tight junction-related factors, were evaluated. LP06CC2 slightly reduced the adipose tissue mass. Further, it dose-dependently decreased plasma total cholesterol (TC). The HFD tended to increase the plasma level of endotoxin and suppressed intestinal ZO-1 expression, whereas a low LP06CC2 dose increased ZO-1 expression and tended to reduce the plasma lipopolysaccharide level. Furthermore, a low LP06CC2 dose facilitated a moderate accumulation of Lactobacillales, a significant decrease in Clostridium cluster IV, and an increase in Clostridium cluster XVIII. The results obtained from analyzing the bile acids (BAs) in feces and cecum contents exhibited a decreasing trend for secondary and conjugated BAs in the low LP06CC2-dose group. Moreover, a high LP06CC2 dose caused excess accumulation of Lactobacillales and failed to increase intestinal ZO-1 and occludin expression, while the fecal butyrate level increased dose dependently in the LP06CC2-fed mice. Finally, an appropriate LP06CC2 dose protected the intestinal barrier function from the HFD and modulated BA metabolism.