In this research, binary-level control topology is designed in which lower-level control frameworks with fractional order proportional integral (FPI) controllers are implemented to control dissolved oxygen (SO) in the last three aerobic bioreactors by regulating the air diffusers (KLa) and FLC is implemented for the plant-wide wastewater treatment process. In order to reduce the operational cost index (OCI) and effluent quality index (EQI), novel control combination frameworks are created utilizing a benchmark simulation model (BSM2PSFe) with a struvite unit as the base. This supervisory topology considers the ammonia in the sixth and seventh aerobic bioreactors as a feedback signal to alter the SO set-points (ABAC) in the lower level. On comparing open-loop with six control approaches (CS1, CS2, CS3, CS4, CS5, and CS6) by using different combinations of fractional FPI and FLC. The OCI and EQI are improved in the case of CS4 by 4.9% and 6.8%. Comparing the open loop with CS6, OCI is decreased by 10% with an improved EQI of 1.3%. For all the control scenarios, greenhouse gas flow rates are decreased. Ammonia, total nitrogen, and total phosphorus are improved by 79.2%, 5.8%, and 0.5% respectively.