Worldwide, most of treatment system are retuning sidestreams (SSs) to the plant wastewater head without treatment, and some innovations are only treating centrate. In this study, an innovative process was established to separately treat all SSs away from plant mainstream and return treated sidestream effluents to plant wastewater outfall instead of wastewater head. This innovative process aims to eliminate SSs impacts on full scale A2/O sewage treatment plant. To do so, a novel pilot extended nutrient moving bed biofilm reactor (EN-MBBR) was developed to treat all SSs lines (supernatant gravity thickener, underflow mechanical thickener, and centrate), and SSs elimination on full scale A2/O system was simulated using GPS-X7. The results of two steps innovative treatment showed that 98, 98, 93, 100, 85, 100 and 98% of TSS, BOD, COD, NH4, NO3, H2S and PO4-P were removed from SSs, respectively. The two steps innovative treatment combined degradation, nitrification, and dilution processes. The simulation results proved that eliminating SSs has eliminated hydraulic and pollutants shocks, reduced the volumes of full scale A2/O facilities, and minimized cost and energy. Moreover, the calibrated model was validated with R values more than 0.8 and NMSE values close to zero. To conclude, the innovative process in this study successfully treated SSs separately and eliminated their impacts.