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To evaluate the effect of yoga on the frequency of MetS and its impact on cardiovascular risk markers in climacteric women. We recruited 84 sedentary women between 40 and 65 years diagnosed with MetS. Participants were randomly assigned to a 24-week yoga intervention or control group. We evaluated the frequency of MetS and changes in the individual components of MetS at baseline and after 24 weeks. We also assessed the impact of yoga practices on cardiovascular risk through the following markers: High-sensitivity C-reactive Protein (hs-CRP), Lipid Accumulation Product (LAP), Visceral Adiposity Index (VAI), and Atherogenic Index of Plasma (AIP). The frequency of MetS reduced significantly after 24 weeks of yoga practice (− 34.1%; p < 0.001). Statistical analysis showed that the frequency of MetS was significantly lower in the yoga group (65.9%; n = 27) than in the control group (93.0%; n = 40) after 24 weeks (p = 0.002). Regarding the individual components of MetS, yoga practitioners had statistically lower waist circumference, systolic blood pressure, triglycerides, HDLc, and glucose serum concentrations than the control group after 24 weeks. Yoga practitioners also had a significant decrease in hs-CRP serum concentrations (3.27 ± 2.95 mg/L vs. 2.52 ± 2.14 mg/L; p = 0.040) and a lower frequency of moderate or high cardiovascular risk (48.8% vs. 34.1%; p = 0.001) after 24 weeks of practice. The yoga group had LAP values significantly lower than the control group after the intervention period (55.8 ± 38.04 vs. 73.9 ± 40.7; p = 0.039). Yoga practice demonstrated to be an effective therapeutic to manage MetS and reduce cardiovascular risk in climacteric women. [ABSTRACT FROM AUTHOR]