We examined the virome of Ae. aegypti mosquitoes with and without natural DENV infection in different regions of Colombia. We found that the mosquito virome mainly consists of insect-specific viruses and that infection with different DENV serotypes led to changes in the abundance of viral families and species. The study also identified previously unreported viruses, highlighting the need for ongoing research on the factors that affect the mosquito virome. The results suggest that a better understanding of the complex interactions between arboviruses, ISV, and vectors can help improve our response to mosquito-borne viral diseases.