The reconstruction or regeneration of damaged bone tissue is one of the challenges of orthopedic surgery and tissue engineering. Among all strategies investigated, additive manufacturing by fused deposition modeling (3D-FDM printing) opens the possibility to obtain patient-specific scaffolds with controlled architectures. The present work evaluates in depth 3D direct printing, avoiding the need for a pre-fabricated filament, to obtain bone-related scaffolds from direct mixtures of polylactic acid (PLA) and hydroxyapatite (HA). For it, a systematic physicochemical characterization (SEM-EDS, FT-Raman, XRD, micro-CT and nanoindentation) was performed, using different PLA/HA ratios and percentages of infill. Results prove the versatility of this methodology with an efficient HA incorporation in the 3D-printed scaffolds up to 13 wt.% of the total mass and a uniform distribution of the HA particles in the scaffold at the macro level, both longitudinal and cross sections. Moreover, an exponential distribution of the HA particles from the surface toward the interior of the biocomposite cord (micro level), within the first 80 µm (10% of the entire cord diameter), is also confirmed, providing the scaffold with surface roughness and higher bioavailability. In relation to the pores, they can range in size from 250 to 850 µm and can represent a percentage, in relation to the total volume of the scaffold, from 24% up to 76%. The mechanical properties indicate an increase in Young’s modulus with the HA content of up to ~50%, compared to the scaffolds without HA. Finally, the in vitro evaluation confirms MG63 cell proliferation on the 3D-printed PLA/HA scaffolds after up to 21 days of incubation.