In this work, we compare the antibacterial activity and hydroxyl radical generation of three different titanium dioxide nanostructures (immobilized titania nanoparticles, nanotubes and ultra-thin films) to find the optimum morphology and processing conditions that could enhance their antibacterial response when this kind of materials are used in catalyst fixed-bed reactors design. It was demonstrated that photocatalytic activity not only depends on direct contact of the catalyst with the pathogen, but also on the concentration of oxidizing species that can be generated in the nanostructured material itself. Based on our results of surface compositional analysis and the behavior of titania nanoparticles-based films, it is suggested that morphology of the titanium dioxide film's surface is largely affected by the material affinity to the substrate underneath. After photoluminescence measurements and analysis, an electron transfer mechanism between the titanium dioxide nanoparticles and the spin-on glass matrix where they are embedded, was found to influence the photocatalytic activity of nanoparticle-based films. While it was observed a similar hydroxyl radical generation (determined by pNDA bleaching) in titania nanoparticle-based films and nanotubes in anatase phase, the antibacterial activity was higher in titania nanotubes. This phenomenon is explained by the fact that it has a relatively smooth surface that allows the bacteria to maintain greater contact in comparison with nanoparticle-based films.