Soil amendment with biochar is being promoted as a promising strategy for carbon (C) stabilization and accrual, which are key to climate change mitigation. However, it remains elusive on how biochar addition influences nonbiochar C in soils and its mechanisms, especially in the presence of plants. Here we conducted a 365-day soil microcosm experiment with and without adding ¹³C-labeled biochar into topsoil to quantify changes in nonbiochar C in the topsoil and subsoil in the presence or absence of rice plants and to determine the mechanisms by which biochar controls nonbiochar C accrual in the soil profile. The nonbiochar C content of topsoil was not affected by biochar addition in the absence of rice plants, but was significantly increased by 4.5% in the presence of rice plants, which could result from increases in the soil macroaggregate fraction, iron (Fe)-bound nonbiochar organic C content, and fungal biomass collectively. However, biochar amendment had no effect on the content of nonbiochar organic C in the subsoil. Overall, biochar-plant interactions drive more nonbiochar C sequestration in the topsoil, and the changes of nonbiochar C in planted soils following biochar addition should be quantified to better assess the soil C sequestration potential in agricultural lands.