Introduction: Non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes mellitus (T2DM) are chronic metabolic disorders that are increasingly prevalent globally, posing significant health challenges. Both conditions are linked to obesity, insulin resistance, and sedentary lifestyles, leading to severe complications such as cardiovascular diseases and liver cirrhosis. Exercise is a crucial lifestyle modification that improves metabolic health in these conditions, but the optimal exercise intensity remains debated. This study investigates the effects of different exercise intensities on metabolic health in patients with NAFLD and T2DM to provide insights for tailored exercise prescriptions. Materials and Methods: This randomized controlled trial involved 100 participants with NAFLD and T2DM, divided into two groups: MICT and HIIT, over 12 weeks. Participants were adults aged 30-65 years with confirmed NAFLD and T2DM, and a sedentary lifestyle. Exclusion criteria included other liver diseases, uncontrolled hypertension, severe diabetic complications, recent participation in a structured exercise program, and contraindications to exercise. Participants were randomly assigned to MICT or HIIT, with exercise sessions supervised by certified physiologists. Primary outcomes were liver fat content and insulin sensitivity, while secondary outcomes included lipid profiles, inflammatory markers, feasibility, and safety. Results: A total of 100 participants (50 per group) completed the study with comparable baseline characteristics. Both groups showed significant reductions in liver fat content and improvements in insulin sensitivity, with HIIT showing greater reductions (p=0.01 for liver fat, p=0.02 for insulin sensitivity). HIIT also led to more significant improvements in triglycerides, LDL, HDL, and inflammatory markers compared to MICT. Adherence rates were high in both groups, although slightly lower in the HIIT group, and dropout rates were comparable. Conclusion: Both MICT and HIIT significantly improve metabolic health in patients with NAFLD and T2DM, with HIIT yielding superior outcomes in reducing liver fat, improving insulin sensitivity, enhancing lipid profiles, and decreasing inflammatory markers. These findings support incorporating HIIT into exercise regimens for this population, highlighting its potential for greater metabolic health benefits. Future research should explore the long-term sustainability and broader applicability of HIIT and strategies to enhance adherence and safety.