Summary Background Malnutrition and food insecurity might be driven not only by individual factors but also by contextual conditions, such as area-level deprivation or vulnerability. This study aimed to analyze the association between area-level vulnerability and i) household food insecurity and ii) malnutrition in children in Medellin, Colombia, during the years 2017 and 2018. Methods We obtained data from two different sources: the Living Standards Measurement Survey (LSMS) and the nutrition surveillance system of Medellin. The main outcomes were food insecurity in households with children and anthropometric indicators for children under five. The main predictor was area-level vulnerability. Mixed effects Poisson regression with robust standard errors models were conducted to test the association of quintiles of deprivation with each outcome. Findings Households with children living in areas with the highest deprivation had 1.9 times the prevalence of food insecurity as compared to those living in areas with the lowest deprivation (PR 1.91, 95% CI 1.42–2.57). Similar results were observed for underweight/risk of underweight (PR 1.26, 95% CI 1.11–1.42), stunting/risk of stunting (PR 1.36, 95% CI 1.22–1.53) and stunting (PR 1.93 95% CI 1.55–2.39) among children under five. We found no consistent associations with wasting/risk of wasting or excess weight/risk of overweight across quintiles of deprivation. Interpretation This study sheds light on the role of area-level vulnerability on malnutrition in children in Medellin, Colombia, showing a pattern of increasing prevalence of food insecurity, underweight and stunting by quintile of deprivation.