Emerging and re-emerging mosquito-borne viruses pose a significant threat to global public health. Unfortunately, effective preventive and therapeutic measures are scarce. An in-depth understanding of the mechanisms regulating viral pathogenesis, vector competence, and viral transmission between mammalian hosts and vectors may lay the foundations for new preventive and therapeutic approaches. Here, we summarize the intricate interactions between commensal microbes and mosquito-borne viruses in mammalian hosts and mosquitoes, including how the host gut microbiota influences the pathogenesis of viral infection; how the host skin microbiota affects the attractiveness of hosts to mosquitoes and viral transmission; and how symbiotic microbes, including endosymbiotic bacteria, fungi, and insect-specific viruses in mosquitoes, regulate viral transmission through gut immune regulation and microbe-derived effectors. In addition, we discuss the potential of symbiotic microbe-based interventions to suppress the transmission of mosquito-borne viral diseases.