AbstractLittle information exists about greenhouse gas (GHG) emissions under perennial bioenergy crops (PBCs) with various N fertilization rates. Our objectives were to evaluate the effect of PBCs receiving various N fertilization rates on N2O and CH4 emissions, GHG balance (GHGB), and yield‐scaled GHGB (YSGB) and compare them with an annual crop from 2012–2013 to 2013–2014 in the northern Great Plains. The PBCs were intermediate wheatgrass (IW, Thinopyrum intermedium [Host] Barkworth and Dewey), smooth bromegrass (SB, Bromus inermis L.), and switchgrass (SG, Panicum virgatum L.), and N fertilization rates were 0, 28, 56, and 84 kg N ha−1. The annual crop was spring wheat (WH, Triticum aestivum L.) with 80 kg N ha−1. The N2O flux peaked immediately after planting, fertilization, intense precipitation (>15 mm), and snowmelt. Cumulative N2O flux was greater for SG than IW and SB with 56 kg N ha−1 in 2012–2013 and with 28–84 kg N ha−1 in 2013–2014. The CH4 flux was not affected by treatments. Carbon sequestration rate at 0–30 cm from 2009 to 2019 was greater for IW than other PBCs. The GHGB and YSGB were greater for SG and SB than IW with almost all N fertilization rates in both years. Comparing PBCs and an annual crop, cumulative N2O flux, GHGB, and YSGB were greater for SG than IW, SB, or WH in 2013–2014. The IW can reduce GHG emissions per unit area and per unit crop yield compared to other PBCs and WH.