Panax ginseng is a precious Chinese medicinal plant with a long growth cycle and high medicinal value. Therefore, it is of great significance to explore effective ways to increase its yield and main active substance content to reduce the cost of ginseng, which is widely used in food and clinical applications. Here, we review the key roles of microorganisms in the biological control of ginseng diseases, enhancement of ginseng yield, biotransformation of ginsenosides, and augmentation of ginsenoside bioactivity. The application of microorganisms in P. ginseng faces multiple challenges, including the need for further exploration of efficient microbial strain resources used in the cultivation of ginseng and biotransformation of ginsenosides, lack of microbial application in large-scale field cultivation of ginseng, and unclear mechanism of microbial transformation of ginsenosides. This review provides a deeper understanding of the applications of microorganisms in P. ginseng.