Despite the worldwide growth of class II and III obesity, the factors associated with type 2 diabetes mellitus (T2DM) in these obese individuals are not widely understood. Moreover, no study has investigated these associations in South America. Our study aimed to investigate the prevalence of T2DM and its associated factors, with an emphasis on biochemical parameters and eating habits, in class II and III obese individuals. We also aimed to analyze the correlation between glycemic parameters and body mass index (BMI). Baseline data from a randomized clinical trial (DieTBra Trial) of 150 class II and III obese individuals (BMI > 35 kg/m2) was used. An accelerometer, Food Frequency Questionnaire, and bioimpedance analysis were used to assess physical activity levels, eating habits, and body composition, respectively. Blood was collected after 12 h of fasting. Hierarchical multivariate Poisson regression was performed, and prevalence ratios (PRs) were calculated. Correlations between glycemic parameters (fasting blood glucose, glycosylated hemoglobin, homeostasis model assessment of insulin resistance (HOMA-IR), and insulin) and BMI were also analyzed. The prevalence of T2DM was 40.0% (95% CI, 32.1–48.3), high fasting blood glucose level was 19.33% (95% CI, 13.3–26.6), and high glycosylated hemoglobin was 32.67% (95% CI, 25.2–40.8). Age ≥ 50 years (PR = 3.17, 95% CI, 1.26–7.98) was significantly associated with T2DM; there was a positive linear trend between age and T2DM (p = 0.011). Multivariate analysis showed an association with educational level (PR = 1.49, 1.07–2.09, p = 0.018), nonconsumption of whole grains daily (PR = 1.67, 1.00–2.80, p = 0.049), and high HOMA-IR (PR = 1.54, 1.08–2.18, p = 0.016). We found a high prevalence of T2DM and no significant correlations between BMI and glycemic parameters.