Polyetheretherketone (PEEK) has mechanical properties suitable for the manufacturing of osseointegration implants. However, its biological properties can be significantly improved by surface modification. In this work, the macroscopic surface topography was obtained by 3D printing and then the 3D printed surface was coated with a TiNb layer. The coating made it possible to apply anodic oxidation, by which a surface with defined nanoscale topography was obtained. Thus, a material with a gradient surface topography and suitable chemical composition was prepared. The properties of the surface were analyzed using optical and scanning electron microscopy. The chemical composition was then evaluated by photoelectron spectroscopy. The roughness, the wettability, and the wear resistance of the surface were observed. The adhesion of the coating and the oxide layer was evaluated. The biological activity of samples was analyzed by seeding them with human osteoblast-like Saos-2 cells. The cell adhesion, proliferation, metabolic activity and viability was observed and was statistically evaluated. After this, the functionality of this surface modification was tested by applying it to an implant with a real geometry. The main conclusions show that the nanostructured TiNb layer on 3D printed PEEK significantly improves biological activity.