In bone regeneration, autografts are considered the gold standard used for medical procedures, but several complications might occur for patients treated with autologous tissue due to the limited availability and also possible tissue morbidity. Scaffolds produced by Additive Manufacturing (AM) technologies allows the control of the pore architecture. This results in 3D matrices with controlled mechanical properties matching those of the tissue to be replaced. The use of polymeric nanocomposites with bio-functionalised layered fillers in a 3D printing device is a smart and effective solution for the production of scaffolds for bone regeneration. Biocompatible layered fillers, like hydrotalcites and zirconium phosphate, can be modified through the intercalation of active species with biocidal activity and then dispersed in a proper bioresorbable polymer using the melt blending technique. The exfoliation of these layered fillers into the polymer allows the preparation of bionanocomposites with better mechanical, cell differentiation and drug delivery properties. In this work MgAl-hydrotalcites and zirconium phosphate intercalated with high loading (up to 54 wt%) with ciprofloxacin and gentamicin antibiotics respectively were successfully employed as active fillers of PEOT/PBT copolymer, already used for clinical applications in orthopedic surgery. The fine dispersion of the fillers, confirmed by XRD and SEM/TEM analyses, was obtained using a twin screw extruder in the melt blending process that allows a good exfoliation/intercalation of the layered compounds into the polymeric composite materials. Composites with different loading of active fillers (from 5 to 20 wt%) were prepared and characterized in order to determine the mechanical (tensile, flexural and compression test). The evaluation of the biocidal activity on Staphylococcus epidermidis (Gram +) and Pseudomonas aeruginosa (Gram -) strains was also carried out by means of a Dose Response screening assay.