Synthetic scaffolds for tissue engineering coupled to stem cells represent a promising approach aiming to promote the regeneration of large defects of damaged tissues or organs. Magnetic nanocomposites formed by a biodegradable poly(caprolactone) (PCL) matrix and superparamagneticiron doped hydroxyapatite (FeHA) nanoparticles at different PCL/FeHA compositions have been successfully prototyped, layer on layer, through 3D bioplotting. Magnetic measurements, mechanical testing, and imaging were carried out to calibrate both model and technological processing in the magnetized scaffold prototyping. An amount of 10% w/w of magnetic FeHA nanoparticles represents a reinforcement for PCL matrix, however, a reduction of strain at failure is also observed. Energy loss (absorption) measurements under a radio-frequency applied magnetic field were performed in the resulting magnetic scaffolds and very promising heating properties were observed, making them very useful for potential biomedical applications.