In this letter we report the controlled growth and microstructural evolution of self-assembled nanocomposite multilayers that are induced by surface ion-impingement. The nanoscale structures together with chemical composition, especially at the growing front, have been investigated with high-resolution transmission electron microscopy. Concurrent ion impingement of growing films produces an amorphous capping layer 3 nm in thickness where spatially modulated phase separation is initiated. It is shown that the modulation of multilayers as controlled by the self-organization of nanocrystallites below the capping layer, can be tuned through the entire film.