Objectives: This study aimed to assess the impact of malnutrition on liver and spleen stiffness in children using shear wave elastography (SWE) and to compare the findings with those of healthy controls. Methods: A total of 308 children aged 0–18 years were prospectively enrolled and classified as either malnourished or healthy according to World Health Organization (WHO) growth reference standards (weight-for-height Z-scores for children under 5 years and BMI-for-age Z-scores for those aged 5 years and older). Liver and spleen stiffness measurements were obtained using SWE by a single pediatric radiologist blinded to nutritional status. Statistical comparisons were performed between groups, across malnutrition severity subgroups, and within different age categories. Results: Liver stiffness did not differ significantly between malnourished children overall and healthy controls, but it was markedly higher in those with severe malnutrition compared to mild or moderate cases (p = 0.018). Spleen stiffness was significantly lower in malnourished children aged 0–6 years compared to controls (p < 0.001). Both liver and spleen stiffness values increased with age (p = 0.014 and p = 0.013, respectively). Conclusion: Our findings indicate that malnutrition is associated with age- and severity-dependent alterations in liver and spleen stiffness. Liver stiffness was elevated only in children with severe malnutrition, whereas spleen stiffness was reduced in younger children but not in older ones. SWE may serve as a valuable non-invasive tool for assessing organ-level effects of malnutrition, and these results may guide future research on the reversibility and clinical significance of such changes. (Table presented.)