TiO2 nanotube layers, synthesized by means of Ti foil anodization, have been modified by Si direct current (DC) magnetron sputtering, carried out at different power and deposition time. The performed SEM imaging suggests that two complementary factors (deposition power and time) play an important role for the surface morphology of the silicon structure deposited on TiO2 nanotubes template. The variation of these parameters allows obtaining a specific “macaroni” like morphology, favorable for Si stabilization during its multiple electrochemical cycling in Li-ion electrolyte. The nanostructured Ti/TiO2–Si layers are electrochemically tested for Li-ion insertion/extraction in 1-butyl-1-methylpyrrolidinium bis (trifluoromethyl) sulfonylimide ([BMP][TFSI]) containing 1M Li[TFSI]. The voltammetric measurements show stable initial cycling, involving equal amounts of Si for the three selected deposition conditions. The potential ranges of Si and TiO2 lithiation–delithiation processes are well resolved, which makes a separate estimation of Si and TiO2 capacities from voltammetric data possible. Both factors, Si deposition parameters and substrate type, influence the long term galvanostatic cycling of the samples. It is found that the “macaroni” like structure deposited at 50W/454s on amorphous TiO2 template exhibits a superior constant current cycling. The good electrochemical performance of this sample type is attributed to the specific morphology of the Si deposit and structural stability of the amorphous TiO2 nanotubes.