This paper describes a protocol for evaluating the effect of largescale non-randomized Wolbachia releases on the incidence of dengue‚ Zika and chikungunya in the municipalities of Niterói and Rio de Janeiro‚ Brazil. A controlled interrupted time series analysis of routinely notified suspected and laboratory-confirmed arboviral cases‚ and monitoring of arbovirus activity‚ will enable the measurement of the impact of the intervention at the population level over time. The aim is to test the hypothesis that the establishment of Wolbachia in local Ae. aegypti populations leads to a reduction in arboviral disease burden. Wolbachiareleases are expected to be completed by the end of 2019‚ and the collation and analysis of disease surveillance data will continue until 2023.