The association between vitamin D deficiency and metabolic syndrome (MS) in severe obesity is unclear and controversial. We analyzed serum and dietary vitamin D and their association with MS in 150 adults with class II and III obesity (BMI ≥ 35 kg/m2) from the DieTBra Trial (NCT02463435). MS parameters were high fasting blood glucose, low HDL cholesterol, high triglycerides, elevated waist circumference, and hypertension. Vitamin D deficiency was considered as a level < 20 ng/mL. We performed multivariate Poisson regression adjusted for sociodemographic and lifestyle variables. The prevalence of serum vitamin D deficiency was 13.3% (mean 29.9 ± 9.4 ng/mL) and dietary vitamin D median was 51.3 IU/day. There were no significant associations between vitamin D, serum, and diet and sociodemographic variables, lifestyle, and class of obesity. Serum vitamin D deficiency was associated with age ≥ 50 years (p = 0.034). After a fully adjusted multivariate Poisson regression, MS and its parameters were not associated with serum or dietary vitamin D, except for lower HDL, which was associated with serum vitamin D deficiency (PR = 0.71, 95% CI 0.52–0.97; p = 0.029). Severe obese individuals had a low prevalence of vitamin D deficiency, which was not associated with MS.