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. I compared soil that experienced root-driven weathering, resulting in the formation of discrete rhizosphere zones in deep soil horizons (100-160 cm) of the Santa Cruz Marine Terrace chronosequence (65 ka-226 ka), with adjacent soil that experienced no root growth. Using a combination of radiocarbon, mass spectrometry, Mössbauer spectroscopy, and X-ray spectromicroscopy approaches, we characterized MOA transformations in relation to changes in C content, turnover and chemistry across four soils ranging in age (65 ka-226 ka). We found that the onset of root-driven weathering (65-90 ka) increased the amount of C associated with poorly crystalline iron (Fe) and aluminum (Al) phases, particularly highly-disordered nano-goethite. The increase in C coincided with greater overall C concentrations, longer C residence times, and a greater abundance of microbially-derived C. Continued root-driven weathering (137-226 ka) 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 metal phases. This decline in C associated to poorly crystalline phases coincided with a decrease in C concentrations and potential turnover rates, and a shift toward plant-derived C. In contrast, soil not affected by root-driven weathering showed low amounts of C bound to poorly crystalline Fe and Al phases regardless of soil age and, correspondingly, lower C concentrations and estimated residence times. My results demonstrate that root-driven formation and disruption of poorly crystalline Fe and Al phases directly controls both C accrual and loss in deep soil. Hence root impacts on soil C storage are dependent on soil weathering stage, a consideration critical for predictions of the vulnerability of deep soil C to global change.