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Abstract Background Despite the reported health effects of cardamom on dyslipidemia, hepatomegaly, and fasting hyperglycemia, no human research has studied its potency in non-alcoholic fatty liver disease (NAFLD) as the hepatic part of metabolic syndrome. Our aim was determining the effects of green cardamom (GC) on serum glucose indices, lipids, and irisin level among overweight or obese NAFLD patients. Methods The place of participant recruitment was the polyclinic of the National Iranian Oil Company (NIOC) central hospital in Tehran. Based on the ultrasonography and eligibility criteria, 87 participants were randomly divided into two groups as cardamom (n = 43) or placebo (n = 44). The supplementation was two 500 mg capsules 3 times/day with meals for 3 months. Serum irisin, fasting blood sugar (FBS), insulin (FBI), total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-c), and high-density lipoprotein cholesterol (HDL-c) were measured. Quantitative insulin sensitivity check index (QUICKI) and homeostasis model assessment-insulin resistance (HOMA-IR) were also calculated. Results In comparison with placebo, GC significantly increased irisin, HDL-c, and QUICKI and decreased FBI, TG, LDL-c, HOMA-IR, and the grade of fatty liver (P < 0.05). After adjustment for confounders, the changes were similar (P < 0.05) with an exception for LDL-c which had a trend (P = 0.07). The differences in FBS, TC, and body mass index (BMI) were not significant (P > 0.05). Conclusion GC supplement improved the grade of fatty liver, serum glucose indices, lipids, and irisin level among overweight or obese NAFLD patients. The changes in these biomarkers may yield beneficial effects on NAFLD. Further trials on the efficacy of GC for clinical practice are suggested. Trial registration Iranian Registry of Clinical Trials, IRCT2015121317254N4. Registered 27/12/2015,