We used a novel diffraction-based method to extract the local, atomic-level elastic strain in nanoscale amorphous TiAl films during in situ transmission electron microscopy deformation, while simultaneously measuring the macroscopic strain. The complementary strain measurements revealed significant anelastic deformation, which was independently confirmed by strain rate experiments. Furthermore, the distribution of first nearest-neighbor distances became narrower during loading and permanent changes were observed in the atomic structure upon unloading, even in the absence of macroscopic plasticity. The results demonstrate the capability of in situ electron diffraction to probe structural rearrangements and decouple elastic and anelastic deformation in metallic glasses.