Zika virus (ZIKV) infection during pregnancy can cause neurological manifestations such as microcephaly. The aim of this study was to explore perceptions of ZIKV and mental health in women exposed to ZIKV during pregnancy in Colombia. This was a mixed-methods study based on structured interviews and psychological tests. Structured interviews were transcribed and analysed with Atlas Ti software. A grounded theory approach was applied. Quantitative analysis was performed with Statistical Package for Social Science, SPSS, V. 20. The study was approved by the Ethics Committee of the Universidad de Córdoba, Montería. Seventeen women participated in the study; nine of them were mothers of children with microcephaly. Maternal age ranged from 16 to 41 years old. The main themes discussed during interviews were: feelings, support, sources of information, and consequences on children's health. Women with children affected by microcephaly showed worse mental health compared to women with normocephalic children. Maternal mental health worsened after 24 months from giving birth. Perceptions regarding disease severity and lack of knowledge were considered to affect maternal mental health. Social support and spirituality were key determinants for caregivers. Future research is needed to further study coping mechanisms and mental health outcomes over time by affected populations.