Objectives To establish the association between malnutrition and vaccination and its socioeconomic determinants in children from a post-conflict zone. Methods a sample of 2,183 households with 2,682 children of 0-4 years was extracted from a survey of more than 15,000 persons. Indicators as weight-for-height, height-for-age and weight-for-age were calculated according to the World Health Organization standards. Vaccination status was checked by comparing the report of the vaccination card with the scheme of the Expanded Immunization Plan for the Pentavalent vaccine (Hepatitis B, Haemophilus Influenzae type B and Diphtheria - Whooping cough - Tetanus) for children 2-59 months and the scheme of BCG Tuberculosis and Hepatitis B for children <2 months. A logistic model with clusters per community was estimated to identify factors associated with malnutrition and vaccination. Results The prevalence of low weight, acute and chronic malnutrition was 2.4%, 5.5%, and 8.6% respectively. 96.3% of the children had their vaccines at the right age. Timely vaccination protects against global and acute malnutrition (OR: 0.244 and 0.357 p <0.001). Children with an incomplete vaccination scheme have a 4.6% probability of being underweight, and 12.1% of having acute malnutrition. The education of the mother (OR: 0.543 and 2.269 p <0.001), the socioeconomic level of the household (OR: and 0.811, and 2.631 p <0.001) and the dependency rate of the child under 5 years (OR: 1.22 and 0,546 p <0.001) are common determinants between acute malnutrition and child vaccination status, respectively. Conclusions This article provides evidence of timely vaccination at age as a protective factor for global and acute malnutrition. In addition, it shows the double effect of the socioeconomic conditions of households in the determination of vaccination and the nutritional status of children.