Deformation of ductile crystalline-amorphous nanolaminates is not well understood due to the complex interplay of interface mechanics, shear banding, and deformation-driven chemical mixing. Here we present indentation experiments on 10 nm nanocrystalline Cu-100 nm amorphous CuZr model multilayers to study these mechanisms down to the atomic scale. By using correlative atom probe tomography and transmission electron microscopy we find that crystallographic slip bands in the Cu layers coincide with noncrystallographic shear bands in the amorphous CuZr layers. Dislocations from the crystalline layers drag Cu atoms across the interface into the CuZr layers. Also, crystalline Cu blocks are sheared into the CuZr layers. In these sheared and thus Cu enriched zones the initially amorphous CuZr layer is rendered into an amorphous plus crystalline nanocomposite.