In this study, we employed the nanoindentation technique to evaluate the pop-in events of Si–Ge multilayers under extra-low forces. X-ray diffraction revealed a shift of the peaks of the Ge atoms from 68.70 to 68.50°, due to gradual mixing of previously isolated Si and Ge atoms into an SiGe compound, upon increasing the annealing temperature. Atomic force microscopy images of the vicinity near the triangular indentation mark revealed that the primarily plastic deformation, the pop-in event observed in the load–displacement curve, was based on slightly active dislocation nucleation and propagation during treatment with the artificial indenter. The samples annealed at RT , 400, 500, and 600°C exhibited hardnesses ( H ) of 18.6 ± 1.2, 17.9 ± 1.1, 18.9 ± 1.2, and 15.0 ± 0.8 GPa, respectively, and elastic moduli ( E ) of 220.0 ± 5.2, 224.9 ± 5.4, 220.7 ± 4.5, and 186.7 ± 3.8 GPa, respectively. These values reveal that elastic/plastic contact translation of the Si–Ge multilayer occurred to various extents depending upon the annealing conditions; in addition, the values of h f / h max for the samples annealed at RT , 400, 500, and 600°C were 0.449, 0.416, 0.412, and 0.470, respectively. In a crystal structure, release of the indentation load reflects the directly compressed volume; the total penetration depth into the film was approximately 30 nm with a peak load of 500 μN. Accordingly, the annealed samples can exhibit pop-in after indentation earlier than samples treated merely at RT .