Soils store significant amounts of carbon (C) and thus can play a critical role for mitigating climate change. Crop roots represent the main C source in agricultural soils and are particularly important for long-term C storage in agroecosystems. To evaluate the potential of different farming systems to contribute to soil C sequestration and thus climate change mitigation, it is of great importance to gain a better understanding of the factors influencing root C allocation and distribution. So far, it is still unclear how root C allocation varies among farming systems and whether the choice of management practices can help to enhance root C inputs. In this study, we compared root C allocation in three main arable farming systems, namely organic, no-till, and conventional farming. We assessed root biomass, vertical root distribution to 0.75 m soil depth, and root-shoot ratios in 24 winter wheat fields. We further evaluated the relative importance of the farming system compared to site conditions and quantified the contribution of individual management practices and pedoclimatic drivers. Farming system explained one third of the variation in topsoil root biomass and root-shoot ratios, both being strongly positively related to weed biomass and soil organic C content and negatively to mineral nitrogen fertilization intensity. Root C allocation was significantly higher in organic farming as illustrated by an increase in root biomass (+40%) and root-shoot ratios (+60%) compared to conventional farming. By contrast, the overall impact of no-till was low. The importance of pedoclimatic conditions increased substantially with soil depth and deep root biomass was largely controlled by precipitation and soil texture, while the impact of management was close to zero. Our findings highlight the potential of organic farming in promoting root C inputs to topsoils and thereby contributing to soil organic matter build-up and improved soil quality in agroecosystems.