Templated electrodeposition is an efficient technique for the bottom-up fabrication of nanostructures and can effectively control the size and shape of the electrodeposits. Here, mesoporous silica thin films with highly ordered mesopores and a regular three-dimensional mesostructure were synthesised as templates for electrodeposition. The mesoporous silica films have small mesopores (∼8 nm) and complex mesopore channels (Fmmm mesostructure with the [0 1 0] axis perpendicular to the substrate). Electrodeposition of bismuth, tellurium and bismuth-tellurium was investigated from electrolytes containing [NnBu4][BiCl4], [NnBu4]2[TeCl6] and [NnBu4]Cl dissolved in dry dichloromethane. Top-view SEM images showed Bi, Te and Bi doped-Te nanoparticles in the mesopores and cross-section SEM showed there were a few Te nanowires, in addition to the particle aggregations on the surface. This is a promising observation as it demonstrates the possibility of preparing sub-10 nm nanowires by templated electrodeposition even though the deposits are not uniformly electrodeposited in all the mesopores. EDX shows the deposited Bi-Te nanoparticles were tellurium-rich, XRD shows they were trigonal tellurium (ICSD 65692). A variety of parameters including the choice of pulsed electrodeposition conditions and [NnBu4][BiCl4] concentration (2.25 mM and 3 mM) were investigated in order to control the composition of the deposit. All samples prepared by pulsed electrodeposition showed very low Bi:Te ratio (Bi/Te<0.02), whereas samples deposited for 5 min at −0.6 V achieved high Bi content (Bi/Te=0.49).