The analysis of solar wind material implanted within lunar soil has provided significant insight into the makeup and evolutionary history of the solar wind and, by extension, the Sun and protosolar nebula. These analyses often rely on the tacit assumption that the Moon has served as an unbiased recorder of solar wind composition over its 4.5 billion yr lifetime. Recent work, however, has shown that for a majority of its lifetime, the Moon has possessed a dynamo that generates a global magnetic field with surface field strengths of at least 5 μT. In turn, the presence of such a field has been shown to significantly alter the lunar–solar wind interaction via the formation of a lunar “paleomagnetosphere.” This paleomagnetosphere has implications for the flux of solar wind minor ions to the lunar surface and their subsequent implantation in lunar soil grains. Here we use a three-dimensional hybrid plasma model to investigate the effects of the lunar paleomagnetosphere on the dynamics and precipitation of solar wind minor ions to the lunar surface. The model results show that the lunar paleomagnetosphere can suppress minor ion fluxes to the lunar surface by more than an order of magnitude and strongly fractionates the precipitating solar wind in a complex, nonlinear fashion with respect to both the minor ion charge-to-mass ratio and the surface paleomagnetic field strength. We discuss the implications of these results with respect to both the analysis of trapped material in lunar grains and the semiquantitative 40Ar/36Ar antiquity indicator for lunar soils.