A rapid (≤2 min) and high-yield low-temperature synthesis has been developed for the in situ growth of gold nanoparticles (NPs) with controlled sizes in the interior of halloysite nanotubes (HNTs). A combination of HAuCl4 in ethanol/toluene, oleic acid, and oleylamine surfactants and ascorbic acid reducing agent with mild heating (55 °C) readily lead to the growth of targeted nanostructures. The sizes of Au NPs are tuned mainly by adjusting nucleation and growth rates. Further modification of the process, through an increase in ascorbic acid, allows for the formation of nanorods (NRs)/nanowires within the HNTs. This approach is not limited to gold-a modified version of this synthetic strategy can also be applied to the formation of Ag NPs and NRs within the clay nanotubes. The ability to readily grow such core-shell nanosystems is important to their further development as nanoreactors and active catalysts. NPs within the tube interior can further be manipulated by the electron beam. Growth of Au and Ag could be achieved under a converged electron beam suggesting that both Au@HNT and Ag@HNT systems can be used for the fundamental studies of NP growth/attachment.