Cellular models have provided significant advances on molecular bases of bipartite interactions between either an arbovirus or a bacterial symbiont with a given arthropod vector. However, although an interference phenomenon was evidenced in tripartite interaction arbovirus-symbiont-mosquito vector very little is known regarding the mechanisms involved. Using large-scale proteome profiling, we characterized proteins differentially expressed in Aedes albopictus cells infected by the symbiotic bacterium Wolbachia and the Chikungunya virus (CHIKV). These proteins were mostly related to cellular processes involved in glycolysis process, protein metabolism, translation and amino acid metabolism. The presence of Wolbachia impacted significantly the protein profiles, including sequestration of proteins such as structural polyprotein and capsid viral proteins that may affect replication and assembly of CHIKV in cellulo. This study provides insights into the molecular pathways involved in the tripartite interaction mosquito-Wolbachia-virus and may help in defining targets for the better implementation of Wolbachia-based strategy for disease transmission control.