Mosquitoes transmit pathogens causing 700 000 deaths annually. Microbe-based vector control, which reduces vector populations or blocks pathogen development within vectors, offers an innovative way to lower global morbidity and mortality due to vector-borne disease. This review addresses challenges hindering the widespread adoption of microbe-based vector control in mosquitoes. We consider understudied transmission routes of mosquito-associated microbiota, factors affecting colonization and persistence of candidate microbial control agents in mosquito hosts, and the need for robust tools and methodologies to validate that observations in laboratory populations can be reliably extended to field populations. We highlight how understanding the microbial ecology underlying interactions between mosquitoes and their native microbiota can guide successful vector control efforts in these and other arthropod disease vectors.