Knowledge of soil nitrous oxide (N₂O) and carbon dioxide (CO₂) fluxes in unfertilized perennial bioenergy crops on marginally productive cropland is crucial to understanding their climate mitigation benefits through reduced greenhouse gas (GHG) emissions. The static chamber method was used to quantify and compare N₂O and CO₂ fluxes in miscanthus (Miscanthus giganteus L.), switchgrass (Panicum virgatum L.), and willow (Salix miyabeana L.) to a successional site over two growing seasons. Mean N₂O and CO₂ fluxes ranged from −0.02 to 0.09 µg N₂O-N m⁻² h⁻¹ and 0.01 to 0.27 mg CO₂-C m⁻² h⁻¹, respectively. Whereas mean CO₂ fluxes differed (p < 0.05) among land use types and between growing seasons, mean N₂O fluxes did not differ (p ≥ 0.166) among land use types or between growing seasons. Our findings suggest that N₂O fluxes from unfertilized perennial bioenergy crops such as miscanthus, switchgrass, and willow on marginally productive croplands are comparable to those from marginal croplands left to undergo natural succession with regrowth vegetation. This alleviates concerns that cultivating perennial bioenergy crops on marginal croplands could increase GHG emissions, particularly when fertilization is minimized or eliminated, if these results hold true on a global scale. Additionally, variations in soil available nitrogen (N), moisture, and temperature did not correspond with differences in mean CO₂ fluxes during both growing seasons. This suggests that root respiration accounted for most of the CO₂ fluxes, rather than microbial soil respiration.