We investigated the structure-property relationship of Co2MnSi Heusler thin films upon the irradiation with He+ ions. The variation of the crystal structure with increasing ion fluence has been probed using nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), and associated with the corresponding changes of the magnetic behavior. A decrease of both the structural order and the moment in saturation is observed. Specifically, we detect a direct transition from a highly L21-ordered to a fully A2-disordered structure type and quantify the evolution of the A2 structural contribution as a function of ion fluence. Complementary TEM analysis reveals a spatially-resolved distribution of the L21 and A2 phases showing that the A2 disorder starts at the upper part of the films. The structural degradation in turn leads to a decreasing magnetic moment in saturation in response to the increasing fluence.