Background: The polycystic ovary syndrome (PCOS) was associated with a higher risk of cardiovascular diseases, related to metabolic dysfunction, due to its peculiar hormonal pattern, dyslipidemia, and inflammatory state. This study was aimed to investigate the effects of thylakoid-rich spinach extract supplementation combined with a hypocaloric diet on cardiometabolic risk factors in obese women with PCOS. Methods: In a double-blind, placebo-controlled design, forty-eight participants (age 20–45 years) consumed in random order either a thylakoid-rich spinach extract powder (5g) or a matched placebo (5g starch), given daily combined with the hypocaloric diet for 12 weeks. The samples were collected at baseline and after the end of the supplementation. The primary outcome was the measure of anthropometric changes, glycemic indices, and lipid profile. The secondary outcomes included inflammatory status and blood pressure. Results: Thylakoid-rich spinach extract supplementation combined with the restricted-calorie diet was associated with significant reductions in abdominal obesity indicators, insulin resistance, lipid accumulation product (LAP), and diastolic blood pressure (DBP) (P< 0.05). Significant decreases were also seen in serum triglycerides (TG), insulin, high-sensitivity C-reactive protein (hs-CRP), and total testosterone compared with the placebo group (P< 0.05). However, no significant differences in systolic blood pressure (SBP) and in serum levels of total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein-cholesterol (HDL-C), and fasting blood glucose were evident between groups at the end of study ( P>0.05). Conclusions: Thylakoid-rich spinach extract supplementation combined with the calorie restriction for 12 weeks may improve the cardiometabolic risk factors in obese women with PCOS.Trial registration: The study was approved by the Ethics Committee of Research Vice-chancellor of Tabriz University of Medical Sciences, Tabriz, Iran, and was registered in the Iranian Registry of Clinical Trials (IRCT20140907019082N9).