Multifunctionality of nanotubes (NTs) is essential in biomedical and biotechnological applications, such as drug/gene delivery, bioseparation, and single-molecule detection. Each functionality should be located at optimal positions, depending on their roles such as targeting, tracking, and transporting. This enables avoidance of possible malfunctions or interference caused by having randomly distributed multiple groups (e.g., hydrophobic and hydrophilic) in the same space. In the aspect of multifunctionality, however, a general selective partial functionalization method of NT inner surfaces still remains a challenge. For this reason, we investigated a selective partial functionalization method of NTs using controlled gold nanoparticle (Au NP) diffusion in nanotubes and the preparation method of Au-capped silica nanotubes. Silica nanotubes (SNTs) were prepared using template sol-gel synthesis, and the inside of SNT was selectively modified with (3-trimethoxysilylpropyl) diethylenetriamine (DETA-silane). Au NPs of 2-nm size were then incubated with SNTs with DETA layer inside. Spontaneous diffusion of negatively charged Au NPs from bulk into the positively charged nanochannels of SNTs led trapped Au NPs onto the inner surface of SNTs. The degree of functionalization was controlled by the channel diameter, Au NP concentration, and solvent type. These SNTs partially modified with Au NPs were then used for localized selective chemical functionalization of SNTs. This was accomplished by the reaction between thionylated Au NPs trapped on the inside of SNTs and Alexa555-maleimide. Au-capped SNTs were prepared from SNTs with Au NPs inside by seed-mediated gold growth.