Rio de Janeiro and Niterói municipalities in southeastern Brazil experience large dengue epidemics every 2 to 5 years, with 100,000 cases notified in epidemic years. Costs of vector control and direct and indirect costs due to the Aedes-borne diseases dengue, chikungunya and Zika were estimated to total $650 million USD in 2016, but traditional vector control strategies have not been effective in preventing arboviral disease outbreaks. The Wolbachia method is a novel and self-sustaining approach for the biological control of arboviral diseases, in which the transmission potential of Ae. aegypti mosquitoes is reduced by stably transfecting them with the Wolbachia bacterium. This paper describes a study protocol for evaluating the effect of large-scale non-randomised releases of Wolbachia mosquitoes on the incidence of dengue, Zika and chikungunya in the municipalities of Niterói and Rio de Janeiro. This follows a lead-in period since 2014 involving intensive community engagement, regulatory and public approval, entomological surveys, and small-scale pilot releases.