Background Atherogenic index of plasma (AIP) is a strong marker to predict the risk of atherosclerosis and cardiovascular disease (CVD). Diabetes alters the utilization of lipids and lipoproteins which cause diabetes-induced atherogenic dyslipidemia leading to CVD. Objectives The study aims to determine whether yoga intervention influences lipid indices in type 2 diabetes mellitus subjects. Methods A total of 104 persons with type 2 diabetes were included in this hospital-based prospective randomized trial. These were further randomized into non-yoga (n = 52) and yoga (n = 52) groups. Intervention of approximately 40 min yoga practice, minimum 5 times in a week over a period of 6 months, was done in the yoga group. Anthropometric parameters (body mass index (BMI) and waist-to-hip ratio (WHR)) were noted, and serum glucose (fasting and post-prandial) and lipid profile [total cholesterol (TC), triglycerides (TG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), very low-density lipoprotein (VLDL)] were estimated in all the subjects on fully automated analyzer. AIP and the logarithm of molar ratio of triglycerides to high-density lipoprotein cholesterol (TG/HDL cholesterol) were calculated. A statistical analysis was done using paired and unpaired student "t" test. Results A highly significant improvement in AIP was observed in the yoga group when compared before and after yoga intervention. Body mass index also showed a similar trend. A statistically significant decrease in TC, TG, LDL, VLDL, and AIP was observed in persons with diabetes in the yoga group when compared with persons with diabetes in the non-yoga group. The result of the study suggests that 6 months of yoga intervention resulted in a significant decline in AIP in persons with type 2 diabetes (p < 0.001). Conclusions Our study concluded that yoga intervention targets elevated lipid levels and aids in correcting dyslipidemia in person with diabetes.