We have selectively hydrophobized halloysite nanotube lumens for efficient loading with a flame retardant for controlled releasing composite materials. The inner lumen of octadecylphosphonic-acid-modified halloysite was loaded with hydrophobic bisphenol-A bis(cliphenyl phosphate). This flame retardant was released from the clay nanotubes in linear fashion over 60 h demonstrating the system potential utility as effective nanocontainers for smart composite systems.