In this research, the effect on the greenhouse gases (GHG) emissions from biological wastewater treatment plants (WWTP) operation by implementing an integrated supervisory control framework on the bench-mark simulation model 2 gas (BSM2G) platform is studied. Ammonia based aeration control is considered for improving the efficiency of the nitrification process and also nitrate control is considered to enhance the performance of the overall plant. Different control strategies are proposed by considering PI control, Model Predictive control and Fuzzy controllers. A notable change is observed in GHG emissions due to bio-treatment because of the impact of control strategies on N2O emissions during denitrification with respect to the nitration where dissolved oxygen (DO) control alone is considered. In addition, when the nitrate loop is considered, a better change is observed in the overall plant performance. On comparison with other approaches, the proposed control strategies resulted in a reduction in the GHG emissions with marginal effect on the other performance indexes effluent quality index (EQI) and operational cost index (OCI).