Recently, polyether ether ketone has raised increasing interest in research and industry as an alternative material for bone implants. This polymer also has some shortcomings, as it is bioinert and its surface is relatively hydrophobic, causing poor cell adhesion and therefore slow integration with bone tissue. In order to improve biocompatibility, the surface of polyether ether ketone-based implants should be modified. Therefore, polished disc-shaped polyether ether ketone samples were surface-modified by direct current magnetron sputtering with ultrathin titanium and zirconium coatings (thickness < 100 nm). The investigation results show a uniform distribution of both types of coatings on the sample surfaces, where the coatings mostly consist of titanium dioxide and zirconium dioxide. Differential scanning calorimetry revealed that the crystalline structure of the polyether ether ketone substrates was not changed by the coating deposition. Both coatings are amorphous, as shown by X-ray diffraction investigations. The roughness of both coating types increases with increasing coating thickness, which is beneficial for cell colonization. The coatings presented and investigated in this study improve wettability, increasing surface energies, in particular the polar component of the surface energies, which, in turn, are important for cell adhesion.