Paleo-detectors are a proposed experimental technique to search for dark matter by reading out the damage tracks caused by nuclear recoils in small samples of natural minerals. Unlike a conventional real-time direct detection experiment, paleo-detectors have been accumulating these tracks for up to a billion years. These long integration times offer a unique possibility: by reading out paleodetectors of different ages, one can explore the time-variation of signals on megayear to gigayear timescales. We investigate two examples of dark matter substructure that could give rise to such time-varying signals. First, a dark disk through which the Earth would pass every ∼45 Myr, and second, a dark matter subhalo that the Earth encountered during the past gigayear. We demonstrate that paleo-detectors are sensitive to these examples under a wide variety of experimental scenarios, even in the presence of substantial background uncertainties. This paper shows that paleo-detectors may hold the key to unraveling our Galactic history.