Subsoils are characterized by low concentrations of organic carbon (OC). Nevertheless, they contain more than half of the global soil OC because of their large volume. This discrepancy suggests that subsoils might further sequester carbon (C), thus acting as potential sinks for atmospheric C. Plant roots and associated rhizodeposits are a major OC input source to subsoils. However, whether and how increased OC inputs via plant roots to subsoils affect soil C sequestration mechanisms remains unclear. Here we set up a pot experiment with European Beech (Fagus sylvatica L.) seedlings to investigate the effect of tree roots and associated rhizosphere development on soil aggregation and C allocation in topsoil vs. subsoil material collected from three forest sites of different parent materials. Over a 5-month growth period, the seedlings developed a dense root system transforming the whole soil volume into root-affected (i.e., rhizosphere) soil. Keywords: Soil organic carbon; Soil fungi; Rhizosphere; Water-stable aggregates; Aggregate fractionation; Carbon storage