In recent years, the relationship between microbes and tumors has led to a new wave of scholarly pursuits. Due to the growing awareness of the importance of microbiota, including those within tumors, for cancer onset, progression, metastasis, and treatment, researchers have come to understand that microbiota and the tumor microenvironment together form a dynamic and complex ecosystem. Liquid biopsy technology, a non-invasive and easily repeatable method for sample collection, combined with emerging multi-omics techniques, allows for a more comprehensive and in-depth exploration of microbial signals and characteristics in bodily fluids. Microbial biomarkers hold immense potential in the early diagnosis, treatment stratification, and prognosis prediction of cancer. In this review, we describe the significant potential of microbial biomarkers in liquid biopsy for clinical applications in cancer, including early diagnosis, predicting treatment responses, and prognosis. Moreover, we discuss current limitations and potential solutions related to microbial biomarkers. This review aims to provide an overview and future directions of microbial biomarkers in liquid biopsy for cancer clinical practice.