Traditional wastewater treatment processes, such as activated sludge and trickling filters, generally face short-term dynamic operational instability and low removal efficiencies of nutrients along with high energy consumption. Dealing with these problems, integrated biological systems which maintain stable performance under the changing load should be developed. The objective of this study was to design a bio-carrier-contained A2O based advanced process train for improved removal efficiency of organic matter and nutrient from municipal wastewater. Two pilot scale plant configurations, Setup-1 (three stage aerobic configuration with 30% fill of carrier) and Setup-2 (A2O process in which carriers were present in the aerobic zone), were fed at a flow rate of 100 L day⁻¹ and hydraulic retention time (HRT) was set to 6–8 h. The progressive acclimation and stabilization of biofilm was reached for Setup-1, where COD removal increased from 73.7 to over 85 %, BOD removal rose from 86.7 % to above 92 % and TSS reduction achieved 90 %. The system was operated at neutral pH (7.2-7.8) and with steady-state biofilm densities of 0.9–1.45 g m⁻². Developed biofilms on the bio-carrier surface showed maximum dry weight production under lower operational temperature conditions (approximately 20 °C). In Setup-2, the removal of COD and BOD were higher than 79 and 87 % respectively, whereas TSS removal was greater than 92 %. Nutrient removal efficiency was considerable, NH₄⁺-N and TN removal efficiencies were near 80 % and 75 %, respectively, while TP removal efficiency was approximately 66 %. Surface biomass density was up to 4.72 g m⁻² indicating later microbial colonization. The bio-carrier-assisted multistage configuration is proved in this study to be an effective, environmentally friendly and economically viable process for advanced treatment of wastewater and nutrient control.