Some obese individuals do not present any metabolic alteration and are considered metabolically healthy (MHO). Adherence to high-quality dietary pattern may favor this phenotype. We aimed to evaluate the association between the adherence to the Mediterranean diet and risk of metabolically unhealthy obesity (MUO) in women. We conducted a cross-sectional study on 2,115 obese women. All patients underwent a medical examination, anthropometric evaluation, bioelectrical impedance, ultrasound measurements of abdominal visceral (VAT) and subcutaneous (SAT) fat, blood sampling and evaluation of adherence to the Mediterranean diet through MEDAS questionnaire. The diagnosis of MHO and MUO was made using the harmonized criteria. A multivariable logistic regression adjusted for age, BMI, fat free mass, ultrasound-estimated VAT:SAT ratio, marital status, education, past diet, antidepressant use, family history of diabetes and cardiovascular disease, menopausal status, smoking, and physical activity was used to assess the association between Mediterranean diet and MUO risk. The prevalence of MHO was 21.2% (N = 449). Compared to MUO women, MHO women were younger, had lower BMI and VAT, and had higher fat free mass and SAT. In the multivariable model, the adherence to the Mediterranean diet was not associated with the risk of MUO (OR = 0.91, 95%CI: 0.62; 1.34, P = 0.624). Given the impact of menopause on metabolic health we also carried out the analysis in pre- and post-menopausal women separately. Higher adherence to the Mediterranean diet was associated with a lower risk of MUO in postmenopausal women (OR = 0.55, 95%CI: 0.31; 0.96, P = 0.034). No association was found in premenopausal women (OR = 1.18, 95%CI: 0.70; 1.99, P = 0.532). In conclusion, adherence to the Mediterranean diet was associated with a better metabolic health in postmenopausal women. Further studies are needed to confirm the ability of the Mediterranean diet in promoting maintenance of the healthy phenotype and reversion from MUO.