The purpose of this study was to produce and characterize Hydroxyapatite/Zinc Oxide/Palladium (HA/0.05 wt% ZnO/0.1 wt% Pd) nanocomposite scaffolds and study their mechanical and antibacterial properties, biocompatibility and bioactivity. The initial materials were developed using sol-gel and precipitation methods. Scaffolds were characterized using atomic absorption analysis (AA), scanning electron microcopy (SEM), energy dispersive spectroscopy (EDS) and transmission electron microscopy (TEM), atomic force microscopy (AFM) and Brunauer−EmmeS−Teller (BET) method. Furthermore, the bioactivity of scaffolds in simulated body fluid (SBF) and the interaction of dental pulp stem cells (DPSCs) with the nanocomposite scaffolds were assessed. Our results showed that the HA/ZnO/Pd (H1), HA/ZnO/Pd coated by 0.125 g chitosan (H2) and HA/ZnO/Pd coated by 0.25 g chitosan (H3) scaffolds possess higher compressive strength and toughness and lower microhardness and density compared to the pure HA (H0) scaffolds. Immersion of samples in SBF showed the deposition of apatite on the surface of the scaffolds. The biocompatibility assay indicated lower cell proliferation on the H1, H2 and H3 in comparison to the H0. The antibacterial results obtained show a significant impact by loading Pd/ZnO on HA in the deactivation of microorganisms in vitro.