Background Dysregulation of calcium signaling is a hallmark of diabetes mellitus (DM) and grain amaranth (AG) has antidiabetic properties. Information on the mechanism of action of AG on blood, renal, and hepatic tissues is sparse, although it continues to be an important alternative medicinal plant in several developing countries. The objective of the study was to determine key changes in calcium levels and s100a1 protein levels and antioxidant and histopathologic changes in blood, renal, and hepatic tissues of male diabetic Wistar rats. Materials and Methods This was an experimental study in which 30 male Wistar rats were kept for 5 weeks (6 groups, N =5). Groups 1-IV had T2DM induced using Nicotinamide and Streptozotocin: Group I, Mixtard®; group II, positive control; group III, 25% AG; group IV, 50% AG. Furthermore, group V consisted of normal rats given 50% GA and group VI was negative control. Blood, renal, and hepatic tissues were collected and analyzed for calcium, s100a1 protein levels, and antioxidant and histopathological changes. Results and Discussion In blood, renal, and hepatic tissue, calcium and s100a1 levels were low during T2DM and these increased following AG supplementation. This was important for improved metabolic processes, thus leading to the low malondialdehyde (MDA) and glutathione peroxidase (GPx) activity in the tissues. Efficient antioxidant status was important for improved calcium signaling mechanisms, thus leading to improved tissue function and protection demonstrating the importance of AG as an alternative medicinal source through the calcium signaling pathway. Conclusion Grain amaranth exerts its antidiabetic properties through improved calcium homeostasis in blood, kidney, and liver.