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The importance of the first 1000 days of life for children has been acknowledged as a crucial phase for malnutrition prevention, where understanding the underlying causes of the problem should be done accordingly. Thus, the study’s objective was to find the factors associated with malnutrition in children under 2 years old. A crosssectional study was conducted involving mothers and children under 2 years old dyads ( n  = 244). A structured and validated socio-demographic and nutrition KAP questionnaire was used whilst weight and height were measured. In this study, 19.3%, 11.8%, and 10.2% of children were stunted, underweight, and wasted, respectively, according to the WHO Growth Reference cut-off. By using multiple logistic regression, this study found that children who have low birth weight and whose mothers have poor nutrition knowledge have higher odds of malnutrition. In conclusion, proper prevention planning considering these associated factors should be done to ensure the effectiveness of the malnutrition prevention program.