This study aimed to evaluate whether being metabolically healthy (MHO) provides protection against micronutrient deficiencies, particularly vitamin B12 deficiency, in obese children and to investigate the relationship between vitamin B12 levels and metabolic health parameters. 296 obese children (mean age: 11.3 years) and 138 age- and sex-matched healthy controls were included. Cases are classified as Metabolically Unhealthy Obese (MUO): One or more of the following criteria: glucose >= 100 mg/dL, triglycerides >= 150 mg/dL, HDL <= 40 mg/dL, or systolic/diastolic blood pressure >= 95th percentile, and MHO: absence of all these criteria.Vitamin B12 was categorized as deficient (< 148 pmol/L (200 pg/mL)), borderline (148-221 pmol/L(200-300 pg/mL)), or sufficient (> 221 pmol/L(> 300 pg/mL)). Using multivariate regression, vitamin B12 levels and metabolic indicators were examined. Of obese children,54.3% were in MUO.MHO and MUO groups had similar vitamin B12 levels(p = 0.051) but considerably lower than the healthy controls. Vitamin B12 insufficiency was detected in 34.3% of obese children compared with 16.1% of controls (p = 0.015). MHO group had a mean B12 level of 281.6 pg/mL, considerably lower than the controls(388.5 pg/mL; p = 0.001).Higher BMI SDS raised B12 insufficiency risk by 4.3-fold (OR = 4.307). Multivariate logistic regression analysis identified statistically significant associations between vitamin B12 deficiency and free T4 (p < 0.001, OR:0.001), AST (p = 0.011,OR:0.897), triglycerides (p = 0.032,OR:1.054), HDL (p = 0.029, OR:0.847), TG/HDL(p = 0.017,OR:0.092), and uric acid (p = 0.047,OR:1.491). Vitamin B12 deficiency is more common in obese children than in healthy controls, regardless of metabolic phenotype. Being metabolically healthy does not appear to offer protection against low vitamin B12 levels. Increased adiposity and associated metabolic alterations may also contribute to vitamin B12 deficiency. These findings underscore the importance of routinely monitoring micronutrient deficiencies in childhood obesity.