Metabolic syndrome, a prediabetic and precardiovascular pathologic condition that begins early in life, tracks into adulthood and magnifies with age. Randomized controlled trials evaluating efficacy of yoga-based lifestyle vs. dietary intervention on metabolic syndrome are lacking. Here, the efficacy of a 12-week yoga-based lifestyle intervention vs. dietary intervention on cardio-metabolic risk factors and metabolic syndrome risk scores have been assessed in Indian adults with metabolic syndrome. In this two-arm, open label, parallel group, randomized controlled trial, 260 adults (20-45 years) diagnosed with metabolic syndrome as per joint interim statement, 2009 were randomized to yoga-based (including diet) lifestyle or dietary intervention alone (n = 130, each) for 12 weeks. Primary endpoints were the 12-week changes in cardio-metabolic risk factors and metabolic risk scores. The secondary endpoints were the 12-week changes in the proportion of subjects recovered from metabolic syndrome, dietary intake, and physical activity. Intent-to-treat analysis was performed including all the subjects with baseline data with imputed missing data. Treatment × time interaction showed yoga-based lifestyle intervention had a greater treatment effect over dietary intervention by significantly reducing waist circumference, continuous metabolic syndrome z-score, and dietary intake/day while significantly increasing physical activity. High-density lipoprotein cholesterol showed a significantly greater reduction following dietary intervention than yoga-based lifestyle intervention. A significantly greater proportion of subjects recovered from metabolic syndrome in yoga-based lifestyle (45.4%) vs. dietary intervention group (32.3%). A 12-week yoga-based lifestyle intervention is more efficacious than usual dietary intervention in improving cardio-metabolic risk factor and metabolic risk score in Indian adults with metabolic syndrome.