BACKGROUND A structured bed reactor subjected to intermittent aeration (SBRIA) is a new reactor configuration that simultaneously promotes the removal of COD and nitrogen in a single reactor. Although studies have shown positive results with this reactor model, some reactor construction and operation parameters remain empirical. This study aimed to optimise the support material diameter and bed porosity for simultaneous COD and total nitrogen (TN) removal in an SBRIA. RESULTS Support material diameter and bed porosity did not affect COD removal and nitrification efficiencies, which achieved average values of 80% and 90%, respectively. However, the denitrification and TN removal efficiencies were significantly affected. The highest denitrification and TN removal were achieved by adopting a support material diameter of 3 cm and 60% of bed porosity. CONCLUSION The response surface methodology demonstrated that the increase in the support material diameter had a positive effect on denitrification due to the existence of an anoxic zone inside the PU foam. Conversely, when the system was operated at low support material diameters, the increase in the bed porosity increased the denitrification process, improving the overall TN removal. © 2021 Society of Chemical Industry (SCI).