Sequencing batch reactors are usually preferred as small wastewater treatment systems. We have demonstrated that using frequent enough switching between aerobic and anoxic conditions, it is possible to by-pass the second step of nitrification. Ammonia is oxidized to nitrite and then is subsequently reduced to nitrogen gas, without producing nitrate. The reason is that nitrite oxidizers have a long recuperation time following an anoxic phase. This type of operation leads to reduced capital and operating costs. In this work we present the results of a pilot-scale SBR built at the municipality of Patras, Greece operated in both 8-hour and 12-hour cycles. It is demonstrated that three pairs of aerobic/anoxic phases with a relative duration of 1:2 (8-hour cycle) and 2:3 (12-hour cycle) secures the desired by-pass of nitrate production.