This pilot study highlights the substantial potential of using isotopically enriched (non-radioactive) metals to study the fate of biodegradable metal implants. It was possible to show that magnesium (Mg) release can be observed by combining isotopic mass spectrometry and isotopic pattern deconvolution for data reduction, even at low amounts of Mg released a from slowly degrading 26Mg enriched (>99%) Mg metal. Following implantation into rats, structural in vivo changes were monitored by μCT. Results showed that the applied Mg had an average degradation rate of 16 ± 5 μm year−1, which corresponds with the degradation rate of pure Mg. Bone and tissue extraction was performed 4, 24, and 52 weeks after implantation. Bone cross sections were analyzed by laser ablation inductively coupled plasma mass spectrometry (ICP-MS) to determine the lateral 26Mg distribution. The 26Mg/24Mg ratios in digested tissue and excretion samples were analyzed by multi collector ICP-MS. Isotope pattern deconvolution in combination with ICP-MS enabled detection of Mg pin material in amounts as low as 200 ppm in bone tissues and 20 ppm in tissues up to two fold increased Mg levels with a contribution of pin-derived Mg of up to 75% (4 weeks) and 30% (24 weeks) were found adjacent to the implant. After complete degradation, no visual bone disturbance or residual pin-Mg could be detected in cortical bone. In organs, increased Δ26Mg/24Mg values up to 16‰ were determined compared to control samples. Increased Δ26Mg/24Mg values were detected in serum samples at a constant total Mg level. In contrast to urine, feces did not show a shift in the 26Mg/24Mg ratios. This investigation showed that the organism is capable of handling excess Mg well and that bones fully recover after degradation.