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Abstract Background Obesity is a significant public health issue associated with various chronic diseases. Research has indicated that chia seeds have the potential to improve cardiometabolic health. However, due to the diversity of research and inconsistencies in study design, further investigation is needed to fully understand their clinical effects on overweight individuals. This review aims to comprehensively analyze the available evidence on the effects of chia seeds on cardiometabolic indices in overweight populations through a meta-analysis. Methods A comprehensive literature search was performed across PubMed, Web of Science, Scopus, and Embase databases from their inception until 01-03-2024 to identify randomized controlled trials (RCTs) evaluating the effect of chia on cardiometabolic indices in overweight subjects. The search strategy incorporated both Medical Subject Headings (MeSH). Following the screening, ten RCTs were finally included. The data, including subject characteristics, study design, and changes in serum biomarkers, were extracted and analyzed using Stata software version 18. Results The meta-analysis results reveal that chia supplementation no significant changes in lipid profile, including triglycerides (TG) (MD: − 5.80 mg/dL, p = 0.47), total cholesterol (TC) (MD: − 0.29 mg/dL, p = 0.95), high-density lipoprotein (HDL) (MD: 1.53 mg/dL, p = 0.33), and low-density lipoprotein (LDL) (MD: 0.63 mg/dL, p = 0.88). Similarity fasting blood glucose (FBG) (MD: − 0.03 mg/dL, p = 0.98), hemoglobin A1c (HbA1c) (MD: − 0.13%, p = 0.13), and insulin levels (MD: 0.45 µIU/mL, p = 0.78). However, chia seed supplementation was associated with a significant reduction in C-reactive protein (CRP) (MD: − 1.18 mg/L, p |