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Abstract Deep soils represent a dynamic interface between surface soils and saprolite or bedrock, influencing water flow, solute and gas exchange, and mineral and organic matter transformations from local to global scales. Root architecture reflects land cover and soil heterogeneity, enabling vegetation access to resources that vary temporally and spatially while shaping soil structure and formation. However, how land use can influence roots and soil structure relatively deep in the subsurface (>30 cm) remains poorly understood. We investigate how cropland‐related land use and subsequent vegetation recovery alter rooting dynamics and soil structure in deeper horizons. Using a large‐scale data set representing multiple land uses as a means of varying root abundance across four soil orders, we demonstrate that B horizon root loss and regeneration are linked to changes in multiple soil structural attributes deep within soil profiles. Our findings further suggest that the degree of soil development modulates the extent of structural transformations, with less‐developed soils showing greater susceptibility to root‐associated structural shifts. The greatest change in structural development and distinctness was observed in Inceptisols, while Ultisols exhibited the least change. Such soil structural changes affect water flowpaths, carbon retention, and nutrient transport throughout the subsurface. This work thus underscores the need for Earth system models to capture dynamic soil structural attributes that respond to land‐use change. We suggest that changes in deep‐rooting abundance, such as those accelerating in the Anthropocene, may be an important agent of subsurface structural change with meaningful implications for contemporary and future ecosystem feedbacks to climate.