Genesis, a member of NASAs Discovery Mission program, is the world’s first sample return mission since the Apollo program to bring home solar matter in ultra-pure materials. Outside the protection of Earth’s magnetosphere at the Earth–Sun Lagrange 1 point, the deployed sample collectors were directly exposed to solar wind irradiation. The natural process of solar wind ion implantation into a highly pure silicon (Si) bulk composition array collector has been measured by spectroscopic ellipsometry and scanning transmission electron microscopy (STEM). Ellipsometry results show that bulk solar wind ions composed of approximately 95% H+, 4% He+ and <1% other elements physically altered the first 59–63 nm of crystalline silicon substrate during 852.8 days of solar exposure. STEM analysis confirms that the solar accelerated ions caused significant strain and visible structural defects to the silicon structure forming a 60–75 nm thick irradiation damage region directly below the surface SiO2 native oxide layer. Monte Carlo simulations of solar wind H, He, C, O, Ne, Mg, Si and Fe ion collisions in the Si collector with fluences calculated from the Genesis and ACE spacecrafts were used to estimate the energy deposited and Si vacancies produced by nuclear stopping in a flight-like Si bulk array collector. The coupled deposited energy model with the flown Genesis Si in situ measurements provides new insight into the basic principles of solar wind diffusion and space weathering of materials outside Earth’s magnetosphere.