The microstructure of ion-implanted crystals is profoundly dictated by mechanical strain developing in interplay with structural defects. Understanding the origin of strain during the early stages of development is challenging and requires accurate measurements and modeling. Here, we investigate the mechanical strain in H-implanted Si. X-ray diffraction analysis is performed to measure the mesoscopic out-of-plane strain and dark-field electron holography to map strain in two-dimensions (2D) with nanometer spatial resolution. Supported by finite element method modeling, we propose that the mean strain field is explained by overlapping and averaging discrete strain fields generated by sub-nanoscopic defects that are intimately related to the H depth concentration.