Aims: Mineral-associated organic matter, mainly derived from microbial by-products, persists longer in soil compared to particulate organic matter (POM). POM is highly recalcitrant and originates largely from decomposing root and shoot litter. Theory suggests that root traits and growth dynamics should affect carbon (C) accumulation into these different pools, but the specific traits driving this accumulation are not clearly identified. Methods: Twelve herbaceous species were grown for 37 weeks in monocultures. Root elongation rate (RER) was measured throughout the experiment. At the end of the experiment, we determined morphological and chemical root traits, as well as substrate induced respiration (SIR) as a proxy for microbial activity. Carbon was measured in four different soil fractions, following particle-size and density fractionation. Results: Root biomass, RER, root diameter, hemicellulose content and SIR (characteristic of N2-fixing Fabaceae species), were all positively correlated with increased C in the coarse silt fraction. Root diameter and hemicellulose content were negatively correlated with C in the POM fraction, that was greater under non N2-fixing Poaceae species, characterized by lignin-rich roots with a high carbon:nitrogen ratio that grew slowly. The accumulation of C in different soil pools was mediated by microbial activity. Conclusions: Our results show that root traits determine C input into different soil pools, mediated primarily by microbial activity, thus determining the fate of soil organic C. We also highlight that C in different soil pools, and not only total soil organic C, should be reported in future studies to better understand its origin, fate and dynamics.