Aedes aegypti mosquitoes are the major vector for human pathogenic viruses such as dengue virus (DENV). Over the past decade, the insect endosymbiotic bacterium Wolbachia pipientis has been introduced in Ae. aegypti populations as an antiviral biocontrol tool, significantly reducing the mosquito-human transmission of Aedes-borne viruses in regions where these mosquitoes are established [1, 2]. Despite the success of this intervention, we still do not fully understand how Wolbachia restricts viruses. Here, we sought to compare two antiviral and one non-antiviral Wolbachia strains stably infecting Ae. aegypti-derived cell lines (Aag2.wMel, Aag2.wAlbB and Aag2.wPip, respectively). Aag2.wMel showed potent antiviral activity dramatically reducing DENV RNA copies and plaque titers compared to its matched Wolbachia-free line. wAlbB also significantly inhibited DENV replication in Aag2 cells but the antiviral activity was weaker than wMel. By contrast, wPip had no impact on viral replication or infectious virus. To investigate the mechanisms underlying the antiviral phenotype, Wolbachia subcellular localization in Aag2 was determined by transmission electron microscopy and immunofluorescence. We observed that wMel and wAlbB were frequently wrapped by the host endoplasmic reticulum (ER) membrane, while wPip remained free in the host cell cytoplasm. The ER-derived organelle, lipid droplets (LDs), were also found to be specifically modulated by antiviral Wolbachia strains, increasing in volume in wMel- and wAlbB-infected cell lines and mosquito tissues compared to those infected with wPip or Wolbachia-free controls. When LD formation was restricted by addition of the small molecule, C75, wMel’s antiviral activity was partially overcome and DENV replication complexes became evident at ER membranes also occupied by Wolbachia. These findings provide the first insight into organelle modification by antiviral Wolbachia strains and demonstrate that Wolbachia-induced lipid redistribution is an important contribution to the antiviral state in Ae. aegypti.