Plant roots are critical weathering agents in deep soils, yet the impact of resulting mineral transformations on the vast deep soil carbon (C) reservoir are largely unknown. Root-driven weathering of primary minerals may cause the formation of reactive secondary minerals, which protect mineral-organic associations (MOAs) for centuries or millennia. Conversely, root-driven weathering may also transform secondary minerals, potentially enhancing the bioavailability of C previously protected in MOAs. Here we examined the impact of root-driven weathering on MOAs and their capacity to store C over pedogenic time scales. To accomplish this, we examined deep horizons (100-160 cm) that experienced root-driven weathering in four soils of increasing ages (65-226 kyr) of the Santa Cruz Marine Terrace chronosequence. Specifically, we compared discrete rhizosphere zones subject to root-driven weathering, with adjacent zones that experienced no root growth. Using a combination of radiocarbon, mass spectrometry, 57Fe Mössbauer spectroscopy, high-resolution mass spectrometry, and X-ray spectromicroscopy approaches, we characterized transformations of MOAs in relation to changes in C content, Δ14C values, and chemistry across the chronosequence. We found that the onset of root-driven weathering (65-90kyr) increased the amount of C associated with poorly crystalline iron (Fe) and aluminum (Al) phases, particularly highly disordered nano-particulate goethite (np-goethite). This increase coincided with greater C concentrations, lower  Δ14C values, and greater abundance of what is likely microbially-derived C. Continued root-driven weathering (137-226kyr) did not significantly change the amount of C associated with crystalline Fe and Al phases, but resulted in a decline in the amount of C associated with poorly crystalline Fe and Al phases. This decline coincided with a decrease in C concentrations, an increase in 14C values, and a shift toward plant-derived C. In contrast, soil not affected by root-driven weathering showed comparatively low amounts of C bound to poorly crystalline Fe and Al phases regardless of soil age and, correspondingly, lower C concentrations. Our results demonstrate that root-driven formation and disruption of MOAs are direct controls on both C accrual and loss in deep soil. This finding suggests that root impacts on soil C storage are dependent on soil weathering stage, a consideration that is critical for future predictions of the vulnerability of deep soil C to global change.