Obesity negatively affects the relationship between markers and micronutrients of bone metabolism. Testing the hypothesis that the metabolically healthy obese phenotype might be protected by those alterations was the aim of this study. A cross-sectional study was carried out in adults with class III obesity classified in Metabolically Healthy Obese (MHO) and Metabolically Unhealthy Obese (MUHO), according to the National Cholesterol Education Program Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (NCEP ATP III) criteria. Anthropometric, biochemical, and clinical variables were analyzed for sample characterization. To evaluate bone metabolism, markers (alkaline phosphatase and parathyroid hormone-PTH) and related nutrients (vitamin D, vitamin B12, calcium, phosphorus, magnesium, potassium and zinc) were analyzed. A total of 223 adults with class III obesity aged 41.20 ± 10.15 years were included. The MHO phenotype was identified in 32.73% of the sample. After logistic regression, it was observed that inadequacies of calcium (OR: 4.11; 95% CI: 2.33-6.66), phosphorus (OR: 3.03; 95% CI: 1.98-5.79), vitamin D (OR: 5.01; 95% CI: 2.92-6.71) and PTH (OR: 5.45; 95% CI: 4.49-6.74) were significantly higher in the MUHO group compared to the MHO Group. This study showed that the MHO phenotype does not protect adults from alterations in markers and micronutrients of bone metabolism. However, the MUHO phenotype presents a higher risk for alterations related to bone metabolism, which can favor the emergence of metabolic bone diseases.