Roots can add significant amounts of carbon (C) to the subsoil, which improves soil physical properties and can mitigate climate change. About 5% of croplands in Germany have been deep-ploughed (30–120 cm) at least once. This can provide better root access to the subsoil and may increase yields, but little is known on the fate of root-derived C in the subsoil (at depth greater than 30 cm) after deep-ploughing. We hypothesized that five decades after deep-ploughing, root-derived C stocks were higher than conventionally ploughed treatments due to better root development. We analysed suberin and cutin monomers as tracers for root- and shoot-derived C at three former deep-ploughed sites in Northern Germany with different soil textures and deep-ploughing depths. Concentrations of suberin monomers in the soil positively correlated with root biomass; this was most pronounced at one sandy site, but had higher variability at the other two sites due to crops with different root systems in the crop rotation, lower root development, and more favourable conditions for C decomposition. Suberin contributed more to the bulk soil organic carbon (SOC) stocks than cutin throughout the soil profile at all sites. The contribution of suberin monomers to the bulk SOC stock at silty site Banteln and the sandy site Essemühle was 38% higher in the deep-ploughed plots than at the reference plot, respectively, these differences were most visible in the subsoil of Essemühle. We conclude that as C stocks and root development increase, suberin SOC stocks also increase, especially in sandy subsoils with low pH.