Innate effector cells are immune cells with protective features and cytotoxic functions that play an important role in regulating the transition from tissue homeostasis to inflammation and the establishment of pathological states, including cancer. However, the tumor microenvironment (TME) can modify the functions of innate cells, reducing their ability to initiate and sustain anti-tumor immune responses. Recent studies have shown that the microbiota can modulate the functions of innate cells in cancer. Commensal microorganisms can interact with innate cells in the TME and release microbial products that have immunomodulatory effects having a crucial role in carcinogenesis, tumor evolution, and response to treatment. Moreover, the microbiota can enhance innate immune responses during anti-cancer therapies, leading to improved therapeutic efficacy. In this review, we discuss the current understanding of the role of the microbiota in shaping host innate immune responses in cancer.