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Microbial fermentation has been widely used to improve the quality and functional composition of food and edibles; however, the approach has rarely been applied to traditional Chinese medicines. In this study, to understand the effect of microbial fermentation on the active ingredients of traditional Chinese medicines, we used <i>Bifidobacterium bifidum</i> and <i>Bacillus subtilis</i> to ferment the traditional Chinese medicine, <i>Cornus officinalis</i> fruit (COF), and determined the levels of active ingredients using HPLC (high-performance liquid chromatography). According to the results, both <i>B. subtilis</i> and <i>B. bifidum</i> substantially increased the amount of gallic acid in the COF culture broth after fermentation; however, the two species of bacteria had no effect on the loganin content. Moreover, the <i>B. subtilis</i> fermentation reduced the contents of ursolic acid and oleanolic acid in the COF broth, whereas the <i>B. bifidum</i> fermentation did not. This study contributes to a better understanding of the mechanism by which microbial fermentation alters the active ingredient levels of traditional Chinese medicines, and suggests that fermentation may potentially improve their functional ingredients.