Intercropping, the simultaneous cultivation of multiple crop species in a single field, increases aboveground productivity due to species complementarity. We hypothesized that intercrops may have greater belowground productivity than sole crops, and sequester more soil carbon over time due to greater input of root litter. Here, we demonstrate a divergence in soil organic carbon (C) and nitrogen (N) content over 7 years in a field experiment that compared rotational strip intercrop systems and ordinary crop rotations. Soil organic C content in the top 20 cm was 4% ± 1% greater in intercrops than in sole crops, indicating a difference in C sequestration rate between intercrop and sole crop systems of 184 ± 86 kg C ha−1 yr−1. Soil organic N content in the top 20 cm was 11% ± 1% greater in intercrops than in sole crops, indicating a difference in N sequestration rate between intercrop and sole crop systems of 45 ± 10 kg N ha−1 yr−1. Total root biomass in intercrops was on average 23% greater than the average root biomass in sole crops, providing a possible mechanism for the observed divergence in soil C sequestration between sole crop and intercrop systems. A lowering of the soil δ15N signature suggested that increased biological N fixation and/or reduced gaseous N losses contributed to the increases in soil N in intercrop rotations with faba bean. Increases in soil N in wheat/maize intercrop pointed to contributions from a broader suite of mechanisms for N retention, e.g., complementary N uptake strategies of the intercropped plant species. Our results indicate that soil C sequestration potential of strip intercropping is similar in magnitude to that of currently recommended management practises to conserve organic matter in soil. Intercropping can contribute to multiple agroecosystem services by increased yield, better soil quality and soil C sequestration.