Aedes albopictus, the invasive Asian tiger mosquito, is responsible for numerous outbreaks of important viruses such as dengue and Zika in various regions of the world. The need for alterative control interventions propelled the development of a novel approach that exploits a natural insect symbiont, Wolbachia; when transferred into non-native hosts, these maternally-inherited bacteria are able to interfere with the transmission of mosquito-borne viruses, and also provide reproductive advantages to the host, offering a promising tool for self-sustaining field applications. Currently, several field trials are ongoing for the primary vector of dengue and several other arboviruses, Aedes aegypti, providing encouraging results. In this study, Ae. albopictus has been targeted for a similar approach: this mosquito species naturally carries two strains of Wolbachia. The introduction of a third, non-native strain made this line less able to transmit dengue and Zika viruses and had an impact on its fitness. The datafile here stored contains the results of the quantitative analyses on Wolbachia density and viral infections, together with the data of the characterisation of the newly generated line.