On 16 April 2016, a 7.8 magnitude earthquake struck coastal Ecuador, resulting in significant mortality and morbidity, damages to infrastructure, and psychological trauma. This event coincided with the first outbreak of Zika virus (ZIKV) and co-circulation with dengue virus (DENV) and chikungunya virus (CHIKV). We tested whether the degree of psychological distress was associated with the presence of suspected DENV, CHIKV, ZIKV (DCZ) infections three months after the earthquake. In July 2016, 601 household members from four communities in Bahía de Caráquez, Manabí Province, Ecuador, were surveyed in a post-disaster health evaluation. Information was collected on demographics, physical damages and injuries, chronic diseases, self-reported psychological distress, and DCZ symptoms. We calculated the prevalence of arbovirus and distress symptoms by community. ANOVA was used to compare the mean number of psychological distress symptoms between people with versus without suspected DCZ infections by age, gender, community and the need to sleep outside of the home due to damages. The prevalence of suspected DCZ infections was 9.7% and the prevalence of psychological distress was 58.1%. The average number of psychological distress symptoms was significantly higher among people with suspected DCZ infections in the periurban community of Bella Vista, in women, in adults 40–64 years of age and in individuals not sleeping at home (p < 0.05). The results of this study highlight the need to investigate the interactions between psychological distress and arboviral infections following natural disasters.