This study examined the effects of cholesterol on mouse intestinal microflora and on isoflavonoids in the cecum and plasma. Dietary cholesterol affects bile acid metabolism and bile acids can influence the intestinal microorganisms. Intestinal microflora appear to play an important role in isoflavone metabolism. We hypothesized that dietary cholesterol changes the metabolism of isoflavonoids and intestinal microorganisms in mice. Male mice were randomly divided into two groups, which were fed a cholesterol-daidzein (CDA) or daidzein (DA) diet (control diet) for 60d. Plasma equol and cecal equol concentrations were significantly higher in the DA group (control group) than in the CDA group. However, plasma cholesterol concentrations were significantly higher in the CDA group compared to the DA group. The composition of cecal microorganisms differed between the two dietary groups. The occupation ratios of Clostridium cluster XI, Clostridium subcluster XIVa, and Lactobacillales were significantly higher in the CDA group. The occupation ratio of Bifidobacterium was significantly lower in the CDA group. This study suggests that dietary cholesterol has the potential to affect the metabolism of equol from daidzein by altering the metabolic activity of the intestinal microorganisms and gut physiological function.