A severe Chikungunya (CHIK) outbreak recently hit several countries of the Indian Ocean. On La Réunion Island, Aedes albopictus was incriminated as the major vector. This mosquito species is naturally co-infected with two distinct strains of the endosymbiont Wolbachia, namely wAlbA and wAlbB, which are increasingly attracting interest as potential tools for vector control. A PCR quantitative assay was developed to investigate Wolbachia/mosquito host interactions. We show that Wolbachia densities are slightly decreased in CHIK virus (CHIKV)-infected females. We measured the impact of CHIKV replication on a lysogenic virus: WO bacteriophage. Our data indicate that WO is sheltered by wAlbB, likely at a single copy per bacteria, and that CHIKV replication is not a physiological stress triggering WO entrance into the lytic cycle.