Surface modification of the Ti6Al4V alloy (ASTM grade 5), with the fabrication of vertically oriented TiO2 nanotubes, has been receiving increasing attention both as a way to provide advanced bioactive features and the ability to act as reservoirs for a localized, controlled drug release. In this work, TiO2 nanotubes were grown on the surface of a Ti6Al4V alloy through electrochemical anodization. An ethylene glycol-based electrolyte containing 0.5 wt.% NH4F and 2.5% (v/v) H2O was used. Post-anodizing heat treatments at 500 °C in air atmosphere were performed to achieve a crystalline oxide layer with a higher mechanical stability. Following these treatments, Zn or Cu nanoparticles were incorporated into the nanotubular structures through electrodeposition processes. Then, the antimicrobial performance of the obtained surfaces was assessed against Staphylococcus epidermidis, a Gram-positive bacterium common in implant-related infections. Lastly, the cytotoxicity of the produced surface was evaluated against MC3T3-E1 mouse pre-osteoblast cells. In general, Cu-doped TiO2 nanotubes presented an almost total antimicrobial action, while Zn doped samples had a lower, but still significant antibacterial effect. However, a highly cytotoxic effect against MC3T3-E1 cells was observed on all anodized samples due to the release of vanadium from the alloy. In spite of this, the surface modification reported in this work can be a valid solution for existing commercially available orthopedic implants, considering that similar solutions were already studied in in vivo assays.