Eating habits may influence inflammatory status and insulin resistance, both involved in the genesis of cardiometabolic diseases; an index of overall diet quality may be useful to identify risk for these diseases. We investigated whether the Healthy Eating Index (HEI-2005), adapted to Brazilian habits (B-HEI), was associated with markers of inflammation, insulin resistance and lipid profile in individuals at cardiometabolic risk. Two hundred and four prediabetic individuals (64.7% women) were enrolled in this cross-sectional study. Anthropometric measurements, 24-h dietary recalls used to calculate the B-HEI, and blood samples were collected. ANOVA was used for comparisons of clinical variables across the B-HEI tertiles and multiple linear regressions employed to test associations between clinical variables and B-HEI total score. Significant trends to decrease mean values of body mass index (BMI) (p = 0.03) and C-reactive protein concentrations (p = 0.02) across the tertiles of B-HEI, but not other biomarkers, were observed. Waist circumference, HOMA-IR and C-reactive protein were inversely associated with the B-HEI (p < 0.05), after adjusting for age, sex, BMI, and physical activity level. Also, a direct association of adiponectin concentrations with B-HEI was detected after adjustments (p = 0.001). Data from this study indicate that the B-HEI may be useful to identify the body adiposity-induced pro-inflammatory status and insulin resistance in individuals at cardiometabolic risk.