Abstract Woodchip bioreactors have the capability to promote the reduction of reactive nitrogen in the nitrate (NO3−) form to dinitrogen (N2), a harmless gas in the atmosphere. Nevertheless, during the reaction the potent greenhouse gas nitrous oxide (N2O) is produced and can be released if denitrification is not complete. The aim of this experiment was to quantify the effect of a soil cap, the concentration of NO3− inflow and drying-rewetting cycles (DRW) on N2O emissions from bench top bioreactors (BTBs, 36.2 × 24.2 × 16.8 cm). The soil cap effect was quantified by comparing the performance of two treatments (n = 3): soil cap (CAP) and soil cap free (UNCAP). The NO3− inflow was simulated by feeding the BTBs with two NO3− concentrations (10 and 5 mg N L−1), and DRW were simulated by saturating and draining the BTBs. Nitrous oxide was quantified in the water samples as well as measured from the surface of the BTBs. The soil cap proved effective at decreasing surface N2O emissions with a reduction of total N2O emissions (calculated as the sum of dissolved N2O and surface N2O emissions) ranging from 30.4 to 42.9%. The NO3− inflow affected dissolved N2O and surface N2O emissions with higher values (average of 3.41 and 0.36 mg m−2 d−1, respectively for CAP, and average of 2.92 and 2.52 mg m−2 d−1, respectively for UNCAP) measured at high NO3− inflow. Drying-rewetting cycles influenced dissolved N2O and surface N2O emissions, with values following rewetting that accounted for more than 56% of the total N2O emissions for both treatments. This study confirmed that soil caps are effective at mitigating N2O emissions and contributed to a better understanding of N2O dynamics induced by two different NO3− inflow concentrations and DRW.