The effect of fatigue on ZrCuAl amorphous metals induced by mechanical cyclic loading is investigated using inelastic neutron scattering and the pair density function analysis of neutron diffraction data. With cooling, the local atomic structure undergoes reorganization under fatigue that is directly related to the number of fatigue cycles. Also under fatigue, suppression in the atomic dynamics is observed as well. A structural restructuring occurs within a 4 Å radius and intensifies with increasing the compression cycles, whereas the vibrational density of states is attenuated as the intensity shifts towards the elastic, zero-energy transfer peak. The combined static and dynamic structural effects are a signature of the microscopic changes brought about by fatigue, and together may be the onset for subsequent behaviors following extended cyclic loading such as fracture. Even after the load is removed, the structural changes described here remain and increase with repeated cyclic loading which is an indication that the lattice deforms even before shear bands are formed.