Abstract Background The State of Ceará, in Northeastern Brazil, suffers from a triple burden of arboviruses (dengue, Zika and chikungunya). We measured the seroprevalence of chikungunya, dengue and Zika and its associated factors in the population of Juazeiro do Norte, Southern Ceará State, Brazil. Methods A cross-sectional study of analytical and spatial analysis was performed to estimate the seroprevalence of dengue, Zika and chikungunya, in the year 2018. Participants were tested for IgM and IgG against these three viruses. Those with IgM and/or IgG positive tests results were considered positive. Poisson regression was used to analyze the factors associated with positive cases, in the same way that the spatial analysis of positive cases was performed to verify whether the cases were grouped. Results Of the 404 participants, 25.0% (103/404) were positive for CHIKV, 92.0% (373/404) for flavivirus (dengue or Zika) and of these, 37.9% (153/404) samples were classified as probable dengue infection. Of those who reported having had an arbovirus in the past, positive CHIKV cases had 58.7% arthralgia (PR = 4.31; 95% CI: 2.06–9.03; p = 0.000) mainly in the hands, ankles and feet. Age over 60 years had a positive association with cases of flavivirus (PR = 1.29; 95% CI: 1.09–1.54; p = 0.000). Fever, muscle pain, joint pain and skin rash were the most reported symptoms (46.1, 41.0, 38.3 and 28.41%, respectively). The positive cases of chikungunya and dengue or Zika were grouped in space and the city center was most affected area. Conclusions Four years after the introduction of CHIKV, where DENV has been in circulation for over 30 years, 1/4 of the population has already been exposed, showing the extent of the epidemic. The measured prevalence was much higher than that reported by local epidemiological surveillance.