The aim of this study was to investigate the ability of Lactobacillus plantarum EM as a starter culture to control cabbage–apple juice fermentation and to explore the cholesterol‐lowering effects of the fermented juice (EM juice) in rats. L. plantarum EM produced strong antimicrobial activities against bacteria and fungi, suppressing other microorganisms in the fermented juice, and was the dominant organism during fermentation and storage. The EM juice also showed strong and broad‐spectrum antimicrobial activity. Rats fed a high‐fat and high‐cholesterol diet and administered EM juice showed significantly reduced total cholesterol (TC), triglyceride, and LDL‐cholesterol levels, as well as a reduced atherogenic index, lower cardiac factors in serum, and lower TC levels in the liver, while total lipid and TC levels in the rat feces increased. Reverse transcription–polymerase chain reaction analysis revealed that the hepatic mRNA expression of HMG‐CoA reductase decreased and the expressions of cholesterol 7α‐hydroxylase and low‐density lipoprotein receptor increased in rats administered EM juice. The effects of EM juice on rats included inhibition of cholesterol synthesis as well as enhancement of cholesterol uptake and cholesterol excretion. The results of this study indicate that the use of L. plantarum EM as a functional starter culture for juice fermentation exerts microbial control, enhances sanitary safety, and provides beneficial food effects against hypercholesterolemia.