One of the most suitable approaches for the production of inorganic nanotubes is by means of carbon nanotube (CNT) templates coated by atomic layer deposition (ALD). This approach is attractive because it has the potential of controlling the wall thickness down to the Angstroms level. However, it is a recognized fact that the chemistry of the substrate surface can delay the full coverage at the initial stages of the ALD coating process, mainly due to nucleation issues. This is an important issue that might restrict laying down homogeneous coatings within the ultrathin range, which is the foundation for producing self-supported inorganic nanotubes. Here, we explore the early stage of the TiO2 nucleation on CNT templates systematically functionalized with different chemical groups (COOH, OH) or N-doped. The effects of the functionalization on the nucleation process from tetrakis (dimethylamino) titanium and water were meticulously studied by means of transmission electron microscopy. Observations revealed grain-like growth of TiO2 over pristine, purified and -OH-functionalized CNTs. In contrast, COOH functionalization yielded good conformality, which was improved on N-doped CNTs. Results were confirmed by X-rays photoelectron spectroscopy analysis. We recommend either COOH or N-doped CNTs for the production of ultrathin TiO2 nanotubes.