The Healthy Eating Index (HEI) estimates the diet quality, and low HEI scores are associated with adverse bone outcomes. However, the relationship between HEI scores and bone health in individuals who are obese but otherwise healthy or obese with comorbidities remains unclear. We aimed to evaluate the association of HEI scores with bone mineral density (BMD), bone regulating hormones and bone turnover markers in individuals with metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO) phenotypes. This was a cross-sectional analysis of 122 adults who were overweight or obese. A questionnaire was completed to obtain demographic data. Body composition and BMD were assessed by a Dual Energy X-Ray Absorptiometry (DXA) exam. The HEI scores and dietary components were calculated using a 24-h dietary recall. Blood samples were collected for the analysis of serum 25-hydroxyvitamin D (s25OHD), total osteocalcin (OC), parathyroid hormone (PTH), and C-terminal telopeptide (CTx) concentrations. The MHO and MUO phenotypes were classified according to the absence or presence of metabolic abnormalities. The sample mean age was 37.91 ± 12.66 years, 50.8% were men, mean body mass index (BMI) was 30.01 ± 4.63 kg/m2, and 45.9% were classified as the MUO phenotype. The mean HEI scores were 54.42 ± 16.25 and 61.48% had low-diet quality. HEI scores were positively associated with s25OHD in the MUO phenotype group (β = 0.194, 95%CI = 0.038-0.350, p = 0.016). Certain dietary score components, such as fruits, seafood and plant protein, added sugars, whole grains, and fatty acids were also associated with bone health markers. However, HEI scores were not associated with BMD measures, neither with other bone regulating hormones and turnover markers. There was a positive association between HEI scores and s25OHD in adults who were overweight or obese with MUO phenotype. Additionally, the adequate consumption of specific food groups may benefit bone mass and metabolism. These results emphasize the importance of lifestyle interventions encouraging healthy eating habits to prevent s25OHD deficiency, poor bone health, and cardiometabolic complications.