Introduction: Microwave Imaging (MWI) is a promising, non-ionizing diagnostic technique whose imaging performance has been significantly enhanced by the introduction of magnetic nanoparticles (MNPs) as remotely controllable contrast agents. Recently, the diagnostic potential of MNP-enhanced MWI has been successfully applied to tissue engineering to track bone regeneration supported by functional magnetic scaffolds (MaS), which are biomaterials loaded with MNPs. As the implanted scaffold degrades and promotes tissue growth, it releases MNPs, generating a specific time-varying magnetic contrast. Methods: To isolate the magnetic signal from the dominant dielectric background of human tissues, a differential ON-OFF measurement protocol is applied by modulating the MNPs with an external polarizing magnetic field. The ill-posed inverse scattering problem is regularized and solved by applying a Truncated Singular Value Decomposition (TSVD) algorithm to the collected differential scattering data. To assess the capabilities of this technique in a 3D scenario, full-wave simulations of a tomographic system were performed using CST Studio Suite. The architecture features an external magnet and an imaging chamber with antennas placed on its outer surface. This chamber is filled with a matching medium and houses a 3D human forearm phantom with cylindrical MaS embedded within the bone. Multifrequency differential scattering data were collected with an Additive White Gaussian Noise applied to simulate measurement uncertainties. Results: The 3D reconstructions accurately localized the focal spot of the magnetic scaffold within the heterogeneous forearm phantom. Furthermore, evaluating four simulated scaffold degradation stages (from 100% down to 25% infill) demonstrated that the progressive variation can be successfully tracked, revealing a predictable, linear decrease in the normalized peak intensity of the reconstructed magnetic contrast. Conclusions: The proposed tomographic system effectively isolates and tracks the degradation of the magnetic implants. These numerical findings validate the system’s diagnostic capabilities, paving the way for non-invasive monitoring of bone tissue regeneration.