Last decade, three-dimensional printing technology has emerged as a useful tool for meticulously fabricated scaffolds with high precision and accuracy, resulting in intricately detailed biomimetic 3D structures. To this end, nowadays, magnetic scaffolds are becoming increasingly attractive in tissue engineering, due to their ability not only to promote bone tissue formation, bone repair, and regeneration, but at the same time allow for nanoscale drug delivery. Although there has been a lot of research effort on the fabrication of bone scaffolds in the last few years, their perspectives as multifunctional magnetic hyperthermia agents remain an open issue. This emerging, uninvestigated research field requires a carefully designed framework to produce reliable results. This work focuses on establishing such a framework by proposing a standardization protocol with certain experimental steps for an accurate evaluation of the heating efficiency of the 3D printed magnetic scaffolds bone phantoms. The specific indexes of specific absorption rate and specific loss power are carefully determined and calculated here to enhance the differences in the heating experimental approaches that followed until now between magnetic nanoparticles and magnetic bone scaffolds. Meanwhile, the heating evaluation cases that one can find in magnetic hyperthermia are seperatelly defined and analyzed with their suited experimental protocols. Firstly, 3D printed magnetic scaffolds are designed and fabricated. Secondly, they are evaluated as heating carriers. A reliable estimation sequence of the heating efficiency, i.e., the specific absorption rate of the magnetic scaffolds, is introduced, analyzed and discussed in conjunction with the specific loss power, which is the respective quantitative index for evaluating the magnetic nanoparticles’ heating efficacy. Finally, this work proposes how the fabrication procedure of the three-dimensional printed scaffolds can be guided by the magnetic particle hyperthermia literature results, as to increase the scaffolds heating efficiency through printing parameters.