The paper presents an experimental study on a lab scale hybrid moving bed biofilm reactor with intermittent aeration. Specifically, a comparison between two different operating conditions was analyzed: continuous and intermittent aeration. Both continuous and intermittent aeration were monitored and compared in order to get the best operational conditions. The intermittent aeration campaign was sub-divided in three phases with different duration of alternation of aerobic and anoxic times and organic and nitrogen loading rates. The efficiency of N-removal improved by 70% during the intermittent aeration. The best condition was observed with 40 min of aeration and 20 min of no-aeration, an organic loading rate of 2.2 kgCODm−3day−1 and a nitrogen loading rate of 0.25 kgNm−3day−1: under these operational conditions the removal efficiencies for carbon and nitrogen were 93% and 90%, respectively. The derived results provide the basis for WWTP upgrade in order to meet stricter effluent limits at low energy requirements.