Background: The role of coffee consumption in the risk of cardiovascular diseases has been debated for many years. The current study aimed to summarize earlier evidence on the effects of green coffee extract (GCE) supplementation on glycemic indices and lipid profile. Methods: We searched available online databases for relevant clinical trials published up to October 2019. All clinical trials investigating the effect of GCE supplementation, compared with a control group, on fasting blood glucose (FBG), serum insulin, total cholesterol (TC), triglyceride (TG), low-density lipoprotein (LDL), and high-density lipoprotein (HDL) were included. Overall, 14 clinical trials with a total sample size of 766 participants were included in the current meta-analysis. Results: We found a significant reducing effect of GCE supplementation on FBG (weighted mean difference (WMD):-2.35, 95% CI: − 3.78, − 0.92 mg/dL, P = 0.001) and serum insulin (WMD:-0.63, 95% CI: − 1.11, − 0.15 μU/L, P = 0.01). With regard to lipid profile, we observed a significant reduction only in serum levels of TC following GCE supplementation in the overall meta-analysis (WMD:-4.51, 95% CI: − 8.39, − 0.64, P = 0.02). However, subgroup analysis showed a significant reduction in serum TG in studies enrolled both genders. Also, such a significant reduction was seen in serum levels of LDL and HDL when the analyses confined to studies with intervention duration of ≥8 weeks and those included female subjects. In the non-linear dose-response analyses, we found that the effects of chlorogenic acid (CGA) dosage, the main polyphenol in GCE, on FBG, TG and HDL were in the nonlinear fashions.