Metabolic syndrome (MetS) and climacteric symptoms often coexist in middle-aged women, increasing cardiovascular risk and reducing quality of life. Yoga shows promise for improving both metabolic and psychological outcomes, but its long-term effects in this population remain understudied. Therefore, this study evaluated the effects of a structured Shivam Yoga training program over 6, 12, and 24 months on metabolic syndrome (MetS) and menopausal symptoms in climacteric women. A total of 102 women with MetS were assigned to a yoga intervention or control group, with assessments at baseline, 6, 12, and 24 months. Primary outcomes included climacteric symptoms, anthropometric data, and biochemical and clinical parameters. The Yoga group showed a significant reduction in MetS frequency at 6 months (-20.8 %; p = 0.028) and 24 months (-46.0 %; p = 0.007) compared to controls. Fasting glucose decreased significantly at all time points (up to -21.54 mg/dL; p = 0.001), and HDL cholesterol increased at 24 months (+20 mg/dL; p = 0.001). At 24 months, waist circumference, systolic blood pressure, and diastolic blood pressure also declined significantly. Climacteric symptoms improved consistently in the Yoga group, with lower Kupperman Index scores and reductions in nervousness at every follow-up (p < 0.05). Additional improvements included insomnia, depressive symptoms, and palpitations at 6 months, with sustained reductions in palpitations (-32.2 %; p = 0.043) and arthralgia/myalgia (-46.0 %; p = 0.007) at 24 months. These findings suggest that Shivam Yoga may offer sustained benefits for both metabolic health and menopausal symptom relief in women with MetS.