Halloysite nanotubes (HNTs) with immobilized gold (Au) and silver (Ag) nanoparticles (NPs) belong to a class of nanocomposite materials whose physical properties and applications depend on the geometry of arrangements of the plasmonic nanoparticles on HNT’ surfaces. We explore HNTs:(Au, Ag)-NPs as potential nano-templates for surface-enhanced Raman scattering (SERS). The structure and plasmonic properties of nanocomposites based on HNTs and Au- and Ag-NPs are studied by means of the transmission electron microscopy and optical spectroscopy. The optical extinction spectra of aqueous suspensions of HNTs:(Au, Ag)-NPs and spatial distributions of the electric fields are simulated, and the simulation results demonstrate the corresponding localized plasmonic resonances and numerous “hot spots” of the electric field nearby those NPs. In vitro experiments reveal an enhancement of the protein SERS in fibroblast cells with added HNTs:Ag-NPs. The observed optical properties and SERS activity of the nanocomposites based on HNTs and plasmonic NPs are promising for their applications in biosensorics and biophotonics.