Using combined deformation processing, including preliminary mechanical activation followed by consolidation via high-pressure torsion, a multi-layer nanocomposite based on nickel and aluminum is manufactured. The influence of the duration of mechanical activation on its microstructure parameters is investigated by the X-ray diffraction analysis and scanning and transmission electron microscopy. It is found out that nanostructuring of the multi-layer nanocomposite during its manufacture ensures the formation of a high density of phase and grain boundaries. It is shown that this structural transformation is accompanied by an intense strengthening effect.