Halloysite nanotubes (HNTs) can be used as stable support materials for gold and silver nanoparticles (Au/Ag-NPs) without distinction given to the morphology of the tubular HNTs, i.e. polygonal prismatic or cylindrical. The present study aimed to use direct visualization techniques to observe and compare the adsorption sites and behaviors of the two tubular morphologies with both Au- and Ag-NPs. Au/Ag-NPs were surface engineered with methyl-, carboxylate-, or phosphonate-terminated linker groups and reacted with halloysite nanotubes with two different morphologies, forming composite materials HNTs@Au-NPs and HNTs@Ag-NPs. Transmission electron microscopy (TEM), selected area electron diffraction (SAED), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared (FTIR) spectroscopy were used to investigate the sorption reactions. Au-NPs disperse well into individual particles while the Ag-NPs show a tendency to agglomerate, making them less suitable probes for adsorption onto HNTs. The results also indicate that polygonal prismatic HNTs show greater sorption than cylindrical HNTs, where NPs were detected on the external walls of the nanotubes. This sorption is suggested to occur at the steps and edges of the particles, at the termini of the tubes, and in the hollow inner lumina. For the varying linker groups, carboxylate- and phosphonate-derivatized Au-NPs show similar sorption behavior on HNTs, while no surface sorption was observed for the methyl-terminated linkers. This justifies the hypothesis that the carboxylate and phosphonate moieties chemisorb to the hydroxyls of the aluminol groups at the edge sites, steps, and lumina of polygonal prismatic HNTs, identifying these as key anion bonding sites on HNTs, while non-ionic, methyl-terminated Au-NPs do not adsorb. Identification of these specific anionic bonding sites on two different HNT morphologies highlights the importance of HNT morphology in their use as stable support materials in applications such as catalysis, anion sorption, and drug delivery, amongst others.