The Colombian armed conflict has disproportionately affected minorities, especially afro-Colombian communities. However, there is a lack of evidence about mental health of victims. This study aims to describe the prevalence of mental illness and its associated factors in Afro-descendant violence survivors in Buenaventura and Quibdó, Colombia. A cross-sectional study was carried out using data from a previous trial which aimed to reduce mental health symptoms (ClinicalTrials.gov: NCT01856673). Data of 710 adults identified through a snowball sampling technique was analysed. Diagnoses of depression, anxiety, post-traumatic stress disorder (PTSD), and dysfunction were established using adapted versions of the Hopkins Symptoms Checklist and the Harvard Trauma Questionnaire, plus variables identified in a qualitative study. Multivariate regressions were used to identify associated factors with these diagnoses. The prevalence of depression, anxiety and PTSD in both cities was 26.62% (95% confidence interval [95%CI]: 20.30;23.89), 36.53% (95%CI: 30.63;42.36), and 39.15% (95%CI: 33.36;44.83), respectively. Being married and having registered with the government as victim of the conflict were found to be protective factors for depression and PTSD, respectively. Psychological trauma, unemployment, and traumatic experiences, amongst others, were found as risk factors. The Colombian armed conflict, plus disparities and social exclusion, may be associated with mental health morbidity.