Cellulosic bioenergy is a primary land‐based climate mitigation strategy, with soil C storage and N conservation important mitigation elements. Here we present 13 years of soil C and N change under three cellulosic cropping systems: monoculture switchgrass (Panicum virgatum L.), a five native grasses polyculture, and no‐till corn (Zea mays L.). Soil C and N fractions were measured four times over 12 years. Bulk soil C in the 0–25 cm depth at the end of the study period ranged from 28.4 (±1.4 se) Mg C ha−1 in no‐till corn, to 30.8 (±1.4) Mg C ha−1 in switchgrass, to 34.8 (±1.4) Mg C ha−1 in native grasses. MAOM ranged from 60 to 90% and POM from 10 to 40% of total soil C. Over 13 years total C as well as both C fractions persisted under no‐till corn and switchgrass and increased under native grasses. In contrast, POM N stocks decreased 33 to 45% across treatments, whereas MAOM N decreased by less than 13% and only in no‐till corn. Declining POM N stocks likely reflect pre‐establishment land use, which included alfalfa and manure in earlier rotations. Root production and large soil aggregate formation explained 69% (p<0.001) and 36% (p = 0.024) of total soil C change, respectively, and 60% (p = 0.020) and 41% (p = 0.023) of soil N change, demonstrating the importance of belowground productivity and soil aggregates for producing and protecting soil C and conserving soil N. Differences between switchgrass and native grasses also indicate a dependence on plant diversity. Soil C and N benefits of bioenergy crops depend strongly on root productivity and pre‐establishment land use.This article is protected by copyright. All rights reserved