New tools and methods are currently under evaluation by the World Health Organization for preventing arbovirus transmission, such as dengue, Zika, and chikungunya. One promising approach involves deploying Aedes aegypti with the endosymbiotic bacterium Wolbachia pipientis to disrupt arbovirus transmission within endemic urban environments. The release program of mosquitoes with the Wolbachia's wMel strain started in August 2017 in 6.88% of the city area of Rio de Janeiro, where 13.1% of the city's population live (~890,000 inhabitants). The deployment of Wolbachia wMel strain in Rio finished in December 2019 with a suboptimal 32% introgression of wMel strain, which coincided with a 38% and 10% reduction of dengue and chikungunya, respectively. We conducted an independent evaluation during 20 consecutive months to evaluate whether the wMel distribution and frequency would expand or retract. More than 50,000 mosquitoes were sampled in 12 neighborhoods with estimated 500,000 inhabitants, of which 39.2% were Ae. aegypti. In total, 7,613 of 19,427 collected Ae. aegypti were screened individually for wMel. Climate, environmental and insecticide application data was used to model the spatiotemporal introgression of wMel. The routine insecticide rotation adopted by the Brazilian Ministry of Health caused the crash of both wMel-infected and -uninfected populations shortly after an increase in coverage with spinosad. However, the wMel-uninfected mosquitoes recovered soon to levels even higher than before, whereas the wMel-infected failed to recover after the population crash. The well documented fitness cost of wMel in egg hatching leads to the absence of an egg bank necessary to recover after adult population was disrupted. Finally, we observed the mtDNA haplotype associated with released Wolbachia at a frequency of ~25% in field-caught uninfected mosquitoes. The reason underlying the poor introgression of Wolbachia wMel strain is multifold. The adoption of an effective larvicide that crashed both wMel-infected and -uninfected populations, the absence of an egg bank due to high fitness cost of egg hatching in the wMel-infected mosquitoes, a suboptimal Wolbachia invasion before the intervention, and Wolbachia loss synergically contributed to the lower invasion and, by corollary, modest epidemiological outcome in Rio de Janeiro. Our results highlight the need to plan and implement technical guidance on Integrated Vector Management in Brazil prior and during the nationwide release of Wolbachia-infected mosquitoes to optimize dengue mitigation efforts while ensuring the judicious use of resources.