The development of high energy density Li-ion batteries requires to look for electrode materials with high capacity while keeping their stability upon cycling. In this study, amorphous silicon (a-Si) thin film deposited on self-organized TiO2 nanotubes is investigated as negative electrode for Li-ion batteries. Nanostructured composite negative electrodes were fabricated by a two-step cost effective electrochemical process. Firstly, self-organized TiO2 nanotube arrays were synthesised by anodizing of Ti foil. Subsequently, thanks to the use of room temperature ionic liquid, conformal Si layer was electrodeposited on the TiO2 nanotubes to achieve the synthesis of nanostructured a-Si/TiO2 nanotube composite negative electrodes. The influence of the Si loading as well as the crystallinity of the TiO2 nanotubes have been studied in terms of capacity and cyclic stability. For an optimized a-Si loading, it is shown that the amorphous state for the TiO2 nanotubes enables to get stable lithiation and delithiation with a total areal charge capacity of about 0.32 mA h cm−2 with improved capacity retention of about 84% after 50 cycles, while a-Si on crystalline TiO2 nanotubes shows poor cyclic stability independently from the Si loading.