Medical grade titanium alloy, Ti-6Al-4V, with TiO2 nanotubes (TiO2-NTs) grown on the surface and then decorated with silver nanoparticles (Ag NPs) is proposed to enhance the antimicrobial properties of the bone/dental implants. However, the decoration with Ag NPs is not consistent and there are concerns about the direct contact of Ag NPs with human tissue. The aim of this study was to achieve a more even coverage of Ag NPs on TiO2-NTs and determine their biocidal properties against Staphylococcus aureus, with and without a top coat of nano hydroxyapatite (nHA). The decoration with Ag NPs was optimised by adjusting the incubation time of the TiO2-NTs in a silver ammonia solution, and using biocompatible δ-gluconolactone as a reducing agent. The optimum incubation in silver ammonia was 7 min, and resulted in evenly distributed Ag NPs with an average diameter of 47.5 ± 1.7 nm attached to the surface of the nanotubes. The addition of nHA did not compromise the antimicrobial properties of the materials; high-resolution electron microscopy showed S. aureus did not grow on the composite with nHA and with >80% biocidal activity measured by the LIVE/DEAD assay, also limited lactate production. Dialysis experiment confirmed the stability of the coatings, and showed a slow release of dissolved silver (3.27 ± 0.15 μg/L over 24 h) through the top coat of nHA.