Core Ideas Adding N fertilizer increases N2O emission from perennial grasses managed as feedstock. Interseeding clover with perennial grasses reduced N2O emission and yield. Soil organic C storage under grasses may be inadequate to offset fertilizer‐induced N2O flux. Nitrogen management to optimize yield‐scaled N2O flux from established grasses is needed. No soil organic C storage occurred under no‐till corn–soybean rotation to offset N2O flux. Switchgrass (Panicum virgatum L.) and big bluestem (Andropogon gerdardii Vitman) are potential bioenergy feedstocks. Perennial grasses managed as bioenergy feedstock require nitrogenous inputs, which can cause N2O emission and, thereby, alter their effectiveness to mitigate greenhouse gas (GHG) emission. Few studies have measured N2O emission from perennial grasses managed as feedstock. The objectives of this study were to compare N2O flux and soil organic C (SOC) storage between (i) grasses with legume companion crops or with nitrogenous fertilizer, (ii) two grass harvest times (autumn and spring), and (iii) perennial systems and corn (Zea maize L.)–soybean [Glycine max (L.) Merr.] (C–S) rotation, all without tillage. Nitrous oxide flux was measured from May 2009 to May 2012, and SOC was measured in 2000, 2006, and 2011. Big bluestem–clover (Dalea) and switchgrass–clover treatments had dramatically reduced annual N2O emissions and yield‐scaled emissions compared with the respective grasses with urea fertilizer. Cumulative N2O emission was 14 to 40% greater in the big bluestem‐spring and switchgrass‐spring treatments compared with respective autumn‐harvested treatments. The average cumulative emission in fertilized big bluestem and switchgrass treatments (18.5 kg N2O‐N ha−1) exceeded that of the C–S rotation (12.7 kg N2O‐N ha−1). The emission factor (EF) for fertilized grasses averaged 2.5%, corn averaged 1.05%, and C–S rotation averaged 1.9%. The SOC storage by perennial grasses was limited to 0 to 5 cm and thus may not be adequate to offset N2O emission. Nitrogen management refinement is recommended for herbaceous perennials to optimize biomass production and minimize N2O emission.