Background/objectives <p>Feeding difficulties and swallowing dysfunction are common clinical problems in children with inherited metabolic diseases (IMDs); however, evidence in the literature remains limited. This cross-sectional study aimed to evaluate food refusal and swallowing function in children with IMDs receiving diet therapy and to investigate their relationship with malnutrition risk.</p> Subjects/Methods <p>This cross-sectional study included 49 children aged 2–6 years diagnosed with carbohydrate (30.6%) and protein (69.4%) metabolism disorders. The STRONGkids tool was used to evaluate malnutrition risk, while nutritional classification was based on WHO-derived anthropometric Z-scores. Swallowing function was assessed using the Pedi-EAT-10, and food refusal behaviors were evaluated with the Food Refusal Scale. Sociodemographic characteristics, dietary habits and anthropometric measurements were recorded. Logistic regression analysis was performed to determine independent predictors of high malnutrition risk.</p> Results <p>According to STRONGkids results, 85.7% of the participants were at moderate risk and 14.3% were at high risk of malnutrition. Higher Pedi-EAT-10 scores were significantly associated with early complementary feeding, prolonged feeding duration, extended total daily feeding time, and reported feeding difficulties (<i>p</i> &lt; 0.05). Logistic regression analysis demonstrated that Pedi-EAT-10 (OR: 1.125; 95% CI: 1.025–1.236; <i>p</i> = 0.013), selectivity (OR: 1.241; 95% CI: 1.110–1.645; <i>p</i> = 0.044), and neophobia (OR: 1.430; 95% CI: 1.117–1.829; <i>p</i> = 0.005) were independently associated with high malnutrition risk.</p> Conclusion <p>Food refusal behaviors and swallowing dysfunction are significantly associated with malnutrition risk in children with IMDs. Comprehensive assessment of feeding behavior and swallowing function may facilitate early identification of nutritional vulnerability and support individualized dietary management strategies.</p>