Background/Objectives: Magnesium (Mg)-based food supplements contribute to the maintenance of adequate levels of Mg that are essential for overall health and well-being. The aim of this double-blind, randomized, cross-over clinical study was to assess the plasma Mg levels in volunteers following the oral administration of a magnesium-based nutraceutical ingredient, MAGSHAPE^TM microcapsules (Mg-MS), in comparison to other commonly used magnesium sources, including the following: Mg Oxide (MgO), Mg Citrate (Mg-C), and Mg bisglycinate (Mg-BG). Methods: A total of 40 healthy women and men were put on a low-Mg diet for 7 days, and after 8 h of fasting, a blood sample was taken from a digital puncture before (0 h) and 1 h, 4 h, and 6 h after the oral intake of each product. Results: Our results showed that the blood plasma levels of Mg increased significantly at all tested time-points after the oral intake of Mg-MS, while the blood plasma levels of Mg increased significantly only after 1 and 4 h of the oral intake of MgO and Mg-C, respectively. However, no significant increase in Mg levels was observed upon the intake of Mg-BG. Interestingly, the Mg-MS microencapsulation technology was observed to enable a sustained increase in plasma Mg levels over the duration of this study, i.e., 1, 4, and 6 h after oral intake. A direct comparison of the increase in plasma Mg levels over the 6 h period revealed that the Mg-MS microencapsulation technology significantly increased Mg bioavailability compared to the non-microencapsulated MgO. Our study also showed that, compared to the other Mg sources tested, the Mg-MS microencapsulation technology reduced adverse side effects commonly associated with Mg supplementation, specifically with regard to increased intestinal motility and sensations of gastric heaviness following oral administration. Conclusions: Altogether, this clinical study introduced MAGSHAPE^TM microcapsules as a bioavailable and well-tolerated alternative to existing Mg-based ingredients used in food supplements.