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Background: A major cause of morbidity and mortality amongst children in displaced settings is malnutrition. Approximately, 45% of deaths are linked to undernutrition among children under 5 years of age. The study aimed to determine the prevalence and associated factors of malnutrition among internally displaced (IDP) children from 6 to 59 months. Methods: A community-based cross-sectional study with an analytical approach was conducted from May to June 2021. A multistage cluster sampling method was used to select mothers/caregivers and administer a structured questionnaire that consisted of three sections: sociodemographic and environmental characteristics, health-related factors and anthropometric measurements) was used to collect data. Data were analysed using SPSS version 27.0. Bivariate analysis was done at p < 0.20 and logistic regression at a 5% level of significance. Results: Overall, 395 children were enrolled with a mean age of 31.4 ± 9.1 months and 59.0% were males. Findings revealed that 52% of children were malnourished; stunted (22.1%), wasted (4.8%), underweight (6.3%) and overweight (35.4%). Independent predictors of overall malnutrition were the age of the mothers/caregivers (AOR: 8.0, 95% CI: 2.0 – 32.1), children who had not taken all their vaccines (AOR: 2.3, 95% CI: 1.4 –3.8), children not dewormed (AOR: 2.9, 95% CI: 1.3–6.3), Children not exclusively breastfed (AOR = 3.3, 95% CI: 1.1–9.6). Conclusion: The prevalence of malnutrition was high among children living in internally displaced households. Thus, there is a need for vaccination and deworming campaigns, and nutritional and educational intervention programmes to improve both forms of malnutrition: undernutrition and over-nutrition. [ABSTRACT FROM AUTHOR]