Dietary polyphenols, including flavonoids, are abundantly present in a healthy and balanced diet. Evidence for their role in preventing non-communicable diseases is emerging. We examined the association between estimated habitual intake of dietary flavonoid and obesity in a cohort study. After adjusting for potential confounding factors, inverse association between total flavonoid intake and excess weight (BMI ≥25) was found (OR = 0.66, 95% CI: 0.45, 0.99); among individual classes of flavonoids, only flavanones were inversely associated with excess body weight (OR = 0.68, 95% CI: 0.48, 0.97). However, when considering adjustment for dietary factors (adherence to the Mediterranean diet), the associations were no more significant. When considering obesity as the outcome (BMI ≥30), individuals with high intake of total flavonoids and flavonols resulted less likely to be obese (OR = 0.38, 95% CI: 0.21, 0.66 and OR = 0.63, 95% CI: 0.39, 0.99, respectively), even after adjustment for confounding factors. The results of the present study add to the current literature further evidence of the association between higher flavonoid intake and decreased body weight. Further studies are needed to confirm retrieved association.