In most municipal wastewater treatment plants, there is need for the removal of nitrogen, which usually takes place using the combined nitrification - denitrification process. Vigorous recirculation between the aeration and the anoxic tanks is enforced, to ensure complete denitrification. The scope of the present work was to investigate the possibility for nitrification-denitrification process in once-through systems (i.e.: without recirculation), without the need for the addition of extra carbon source (i.e. using the BOD in wastewater as carbon source), using encapsulated microorganisms. The primary aim was to increase the concentration of nitrifiers in the aerated reactor with parallel operation at hydraulic retention times (HRTs) below the doubling time of heterotrophic microorganisms, thus ensuring high ammonia oxidation rate and minimal reduction of organic carbon. The preserved organic carbon may be then used as carbon source at the downstream anoxic reactor. Coagulated and clarified wastewater from the effluent of the primary clarifier of a municipal wastewater treatment plant was used as feed to the system. The system comprised of two reactors (with 2 L working volume each) configured in series. The first one (aerated tank) contained encapsulated nitrifiers, while the second one (anoxic tank) contained encapsulated denitrifiers. The system operated at HRTs 8, 4 and 3 h (calculated individually for each reactor). The experiments indicated that at HRT equal to 8 h, almost all N-NH4+ was converted to N-NO3- in the aerated reactor, while the total nitrogen (TN) concentration was below 2 mg L-1 at the exit of the system. At HRT of 4 h a slight decrease in N-NH4+ removal was observed at the exit of the aerated tank (N-NH4+ concentration was measured 3.7 ± 0.1 mg L-1). At HRT equal to 4 h, N-NH4+ concentration did not change significantly during the downstream treatment in the anoxic tank, while N-NO3- concentration at the exit of the system was 1.4 ± 0.1 mg L-1. At the lowest HRT (3 h), N-NH4+ concentration was measured between 10 and 11 mg L-1, both, at the exit of the aeration tank and at the exit of the system; while, N-NO3- was measured 2.6 ± 0.2 mg L-1 at the exit of the system. On the other hand, BOD and TOC removal in the aeration tank decreased with the decrease of the HRT. BOD concentration at the exit of the anoxic tank measured 30.3 ± 2.2 and 19.4 ± 1.7 mg L-1 for HRTs 8 h or 4 h, respectively, while it was measured 51.6 ± 7.6 mg L-1 at HRT 3 h. On the other hand, TOC concentration at the outlet was measured 17.5 ± 1.2 and 13.2 ± 0.6 for HRTs 8 or 4 h, respectively, while it was measured 31.1 ± 5.6 mg L-1 at HRT equal to 3 h. Analysis of variance (ANOVA) showed significant variations of all measured parameters with the applied HRT, apart from N-NO3- concentration at the exit of the aerated tank. The latter was attributed to the complete oxidation oft N-NH4+ in the aerated tank at all HRTs. Based on the efficiency of the system, the volume of the aeration and denitrification tanks of a wastewater treatment plant using encapsulated microorganisms may be designed 16 times smaller, compared to conventional activated sludge plants, while the need for recirculation between the aerated and anoxic tanks may be completely eliminated.