Arthropod-borne viruses (Arboviruses) like dengue (DENV) or chikungunya (CHIKV) virus are a major threat for public health, responsible for millions of cases each year worldwide. Arboviruses are mainly transmitted by mosquitoes, whose vectorial competence depends on environmental, genetic and immune factors. Recently, it was showed that mosquito microflora, like fungi and bacteria, could also modulate host vectorial competence. This is the case for Wolbachia, an obligatory intracellular Alphaproteobacteria commonly found in arthropods, which was shown to decrease DENV, WNV and CHIKV transmission in mosquito. Nevertheless, the cellular mechanisms of this interaction remain largely unknown. To improve our understanding of the host mechanisms involved in Wolbachia-arbovirus interaction, we used the C6/36 cell line from Aedes albopictus, a competent vector of CHIKV and DENV. We stably infected C6/36 cells with the Wolbachia strain wAlbB, naturally present in Ae. albopictus, then performed CHIKV infections. Results showed that viral replication and infectiosity decrease in the presence of the bacteria compare to cells were Wolbachia was cleared using antibiotic. In light of recent studies suggesting the importance of autophagic process during arbovirus infection, we showed that autophagy was modulated in mosquito during viral and bacterial co-infection, and could partially explain the antiviral effect of Wolbachia. These results must be thorough and extended to other mosquito species to try to decipher the role of mosquito endosymbionts on pathogen transmission.