This study explores the fabrication of bone scaffolds using a composite ink of poly-ε-caprolactone (PCL), polyhydroxybutyrate (PHB) and synthesized fluorapatite (FHAp) via response surface methodology optimization to achieve optimal Vickers hardness number (VHN). Characterization with X-ray diffraction confirms FHAp presence and increased crystallinity post-sintering, while Fourier-transform infrared spectroscopy reveals fundamental material interactions. Results show PCL’s softening effect at higher concentrations, PHB’s contribution to decreasing hardness and FHAp’s significant role in reinforcing the composite. Contour plots demonstrate peak hardness at lower PCL and PHB concentrations (<11% wt/v) with 18% wt/v FHAp. The optimum hardness values were found at PCL, PHB and FHAp of 9.754% wt/v, 9.473% wt/v and 24.608% wt/v, respectively, yielding 185.34 VHN. These findings offer insights into optimizing composite concentrations for tailored mechanical properties crucial in bone scaffold design, advancing regenerative medicine and tissue engineering.