A simple chemical method to assemble peptide nanotubes and simultaneously arrange them into macroscopic bundles is reported. The peptide nanotubes, self-assemblies of the bolaamphiphilic peptide monomer bis(N-alpha -amido-glycylglycine)-1,7-heptane dicarboxylate, appeared in acidic solution within 1 week. In the presence of Ni2+ ions, the bolaamphiphile peptide assembles into well-organized macroscopic bundles of the peptide nanotubes. Addition of EDTA to a suspension of peptide nanotube bundles resulted in disassembly of the bundles into peptide nanotubes with diameters between 40 and 140 nm. A majority of the free amide sites of the peptide nanotubes were involved in the intercalation of nickel ions, which act as bridges to bundle adjacent peptide nanotubes. The covalent bridge of Ni2+ ions with amide groups of the peptide nanotube was confirmed by Raman microscopy.