A 50-year-old male participant with sedentary lifestyle, diagnosed with Metabolic Syndrome (MetS) [obesity, Type-2 diabetes mellitus, hypertension] and hypothyroidism since 2013, was administered integrated Yoga and Naturopathy (IYN) for 6 weeks as a tailor made individualized protocol at the residential integrative medical facility in Bangalore between October and November 2015. The results showed reduction in weight (97.9 kg to 74.6 kg), Body Mass Index (BMI) (35.1 kg/m2 to 27.86 kg/m2), total cholesterol (192 mg% to 145 mg%), triglycerides (153 mg% to 90 mg%), Low Density Lipoprotein (LDL) (124 mg% to 81 mg%), High Density Lipoprotein (HDL) (40 mg% to 46 mg%), fasting blood glucose (110 mg/dl to 75 mg/dl), postprandial glucose (267 mg/dl to 100 mg/dl), glycated hemoglobin (HbA1c) (7.8%-7.1%), Thyroid Stimulating Hormone (TSH) (6.90 μIU/ml to 3.052 μIU/ml). Following the intervention, the anti-hypertensive, oral hypoglycemic, thyroid raising and analgesic medicines were not required to be continued. His knee pain minimized on discharge as observed on a Visual Analog Scale. He had an improved feeling of wellness and overall functional health. All his parameters were within normal range at the 12-weeks follow-up, as he had incorporated the lifestyle program into his daily routine. This case report suggests that lifestyle change by integration of specific non-drug Yoga and Naturopathic intervention is useful in the management of MetS.