Background: Dyslipidemia poses a high risk for cardiovascular disease and stroke in Type 2 diabetes (T2DM). There are no studies on the impact of a validated integrated yoga lifestyle protocol on lipid profiles in a high-risk diabetes population. Methods: Here, we report the results of lipid profile values of 11,254 (yoga 5932 and control 5322) adults (20–70 years) of both genders with high risk (≥60 on Indian diabetes risk score) for diabetes from a nationwide rural and urban community-based two group (yoga and conventional management) cluster randomized controlled trial. The yoga group practiced a validated integrated yoga lifestyle protocol (DYP) in nine day camps followed by daily one-hour practice. Biochemical profiling included glycated hemoglobin and lipid profiles before and after three months. Results: There was a significant difference between groups (p < 0.001 ANCOVA) with improved serum total cholesterol, triglycerides, low-density lipoprotein, and high-density lipoprotein in the yoga group compared to the control group. Further, the regulatory effect of yoga was noted with a significant decrease or increase in those with high or low values of lipids, respectively, with marginal or no change in those within the normal range. Conclusion: Yoga lifestyle improves and regulates (lowered if high, increased if low) the blood lipid levels in both genders of prediabetic and diabetic individuals in both rural and urban Indian communities.