Grape seed extract (GSE) is a flavonoid‐rich supplement, recently discussed as a potential moderator of inflammation and obesity. In this study, we aimed to investigate the effects of GSE supplementation along with a restricted‐calorie diet (RCD), on changes in blood lipid profile, visceral adiposity index (VAI), and atherogenic index of plasma (AIP). We designed a randomized, double‐blinded, placebo‐controlled clinical trial. Forty obese or overweight individuals (25 ≤ body mass index < 40 kg/m2) were randomly assigned to receive GSE (300 mg/day) or placebo, plus RCD, for 12 weeks. We studied the anthropometric measures, biochemical biomarkers and dietary intake within the study timelines. Levels of high‐density lipoprotein cholesterol (HDL‐C) and HDL‐C/low‐density lipoprotein cholesterol (LDL‐C) significantly increased in the GSE group as compared with the placebo group at week 12 (p = .03 and .008, respectively, adjusted for age, sex, energy and saturated fatty acid intake). We also observed a significant reduction in LDL‐C following GSE supplementation in comparison to placebo (adjusted for age, sex and energy intake, p = .04). VAI, AIP, total cholesterol and triglyceride significantly decreased in the GSE group compared with the baseline (p = .04, .02, .01, and .02, respectively). GSE supplementation may have a modulatory role in improving blood lipid profile in obese or overweight individuals, when accompanied by RCD.