Selective fatty acid hydrophobization of the inner surface of tubule halloysite clay is demonstrated. Aqueous phosphonic acid was found to bind to alumina sites at the tube lumen and did not bind the tube's outer siloxane surface. The bonding was characterized with solid-state nuclear magnetic resonance (Si-29, C-13, P-31 NMR), Fourier transform infrared (FTIR), and X-ray photoelectron spectroscopy. NMR and FTIR spectroscopy of selectively modified tubes proved binding of octadecylphosphonic acid within the halloysite lumen through bidentate and tridentate P-O-Al linkage. Selective modification of the halloysite clay lumen creates an inorganic micelle-like architecture with a hydrophobic aliphatic chain core and a hydrophilic silicate shell. An enhanced capacity for adsorption of the modified halloysite toward hydrophobic derivatives of ferrocene was shown. This demonstrates that the different inner and outer surface chemistry of clay nanotubes can be used for selective modification, enabling different applications from water purification to drug immobilization and controlled release.