Gold nanoparticles (Au-NPs) were created in crystalline yttria-stabilized zirconia (YSZ). (100)-, (110)- and (111)-oriented YSZ samples were implanted by 1 MeV Au+ ions at room temperature and fluences ranging from 1.5 × 1016 cm−2 to 7.5 × 1016 cm−2. The prepared Au: YSZ structures were annealed at 1100 °C for 1 h on air to support the Au-NPs coalescence and YSZ structure recovery. Subsequent irradiation with the 10 MeV Si3+ ions with a fluence of 5.0 × 1014 cm−2 was performed to enable gradual modification of Au-NPs. Au-depth profiles and YSZ structure modification in the produced samples were analysed via Rutherford backscattering spectrometry in channelling mode (RBS-C) and X-ray diffraction (XRD). RBS-C showed the gold distributed in the region of about 50–300 nm below the YSZ surface. The disorder was accumulated in the region with Au-NPs and the concentration of the disorder increases as a function of ion implantation fluence. The Zr-disorder was partially decreased after the annealing, while the subsequent Si-ion irradiation increased Zr-disorder again, however, the disorder does not reach values before the annealing. XRD measurement evidenced elastic deformation of the YSZ host lattice in the Au-implanted samples. Optical absorbance showed the appearance of the new absorption band at 550 nm for the Au-ion fluences above 5.0 × 1016 cm−2 ascribed to the Au-NPs formation. After the annealing, the absorption band is shifted to the wavelength of 580 nm which could be connected to the proceeding clustering of Au. The maximum absorption peak intensity increases which is connected to the increasing amount of the Au-NPs. Transmission electron microscopy (TEM) with Energy dispersive spectroscopy (EDS) confirmed the presence of Au-NPs in the implanted layer after the annealing. The subsequent Si-ion irradiation did not change the Au-NP shape which remained spherical with a slight size increase.