The necessity for finding a compromise between mechanical and biological properties of biomaterials spurs the investigation of the new methods to control and optimize scaffold processing for tissue engineering applications. A scaffold composed of ε-polycaprolactone fibers reinforced with carbonated hydroxyapatite (CHAP) dually doped with selenite oxyanions (Se) and cationic gold (Au) was synthesized using the electrospinning technique and studied at different contents of Au. Despite the fact that the amount of the Au dopant was relatively low, variations to it induced significant microstructural changes, affecting the cell response and mechanical properties in return. Au nanoparticles segregated as a separate, ternary phase at the highest Au content, corresponding to x=0.8 in the AuxCa10−1.5x(PO4)5.8(SeO2)0.2−x(CO3)x(OH)2 stoichiometric formula of Au/Se-CHAP. Their appearance coincided with a rapid degeneration in the density and adhesion of osteoblastic cells grown on the scaffolds. In spite of this adverse effect, the cell spreading and proliferation improved with increasing the amount of the Au dopant in the Au/Se-CHAP particles of the scaffold in the x = 0.0–0.6 range, suggesting that the biological effects of Au in the ionic and in the nanoparticulate form on the implant integration process may be diametrically opposite. The addition of Au had a dramatic effect on some mechanical properties, such as toughness and strain at break, which were both reduced twice upon the introduction of Au into Se-CHAP at the lowest amount (x = 0.2) compared to the Au-free composite. The significant variation of physical and biological properties of these composite scaffolds with trace changes in the content of the Au dopant inside the ceramic filler particles is promising, as it provides a new, relatively subtle avenue for tailoring the properties of tissue engineering scaffolds for their intended biomedical applications.