Sprouts are an attractive food product that contains high amounts of nutritional substances and has pro-health features. Sprout consumption has strongly increased despite its potential risk to health due to its microbial load. Both the safety and shelf life of sprouts may be negatively affected by a high microbial load. To reduce the microbial contamination in sprouts before consumption, the initial microbial load on the seeds needs to be controlled. Many herbal sprouts have been recommended for diabetes, and fenugreek is one of these sprouts. Thus, the current experiment aimed at disinfecting fenugreek seeds using microwave (5, 10, and 20 s) and hot water (30, 45, and 60 s) treatments for different durations. The best-disinfected sprouts with the highest nutritional properties were used to evaluate their influence on streptozocin-induced diabetic rats in comparison with fenugreek seed feeding. Microwave treatments showed the highest sprout length, fresh weight, total free amino acids, antioxidants, reducing sugars, and total phenols. Additionally, microwave seed treatments showed the lowest bacteria and mold counts on sprouts produced relative to hot water treatments, and the best seed treatment was a microwave for 20 s, which gave the best values in this respect. Feeding diabetic rats with different fenugreek seeds or sprout rates (0, 5, 7.5, and 10% w/w) improved body weight, restricted the growth of glucose levels, lowered total cholesterol and triglycerides, and improved HDL compared with the positive control group, and fenugreek sprouts at higher rates showed the maximum improvements in blood glucose, total cholesterol, and triglycerides. Treating fenugreek seed with microwave radiation for 20 s to disinfect the seeds before sprouting is recommended for lowering the microbial load with optimum nutritional and antioxidant activity, and feeding diabetic rats with these sprouts at the rate of 7.5 and 10% had promising effects on hyperglycemia and associated disorders.