In this study, biogenic CO2 emissions, COD and other nutrients (i.e. TP, TN and NH+4-N) from aerobic treatment in municipal Wastewater Treatment Plants (WWTP) were quantified and reduced by phycoremediation using a mixotrophic co-cultivation of Chlorella vulgaris and activated sludge. It has been shown that the microalgae sludge consortium (A-ASR, R1) outperformed the normal-activated sludge system (ASR, R2). In fact, estimated biogenic CO2 emissions with algae mark 1.20-fold higher removal, COD marks 1.40-fold higher removal, TP marks 1.70-fold higher removal, and NH4+-N marks 1.40-fold higher removal, compared to normal activated sludge (ASR, R2). Meanwhile, due to aeration, NO3-N concentration increased in both reactors because some Ns were oxidized through nitrification. Furthermore, COD increased again during C. vulgaris stationary growth; thus, activated sludge addition every 4 days (optimal time) was implemented to maintain algae-bacteria balance. The results suggest that integrating the treatment of GHG emissions and water pollutants in a single, concurrent process can significantly enhance the sustainability and efficiency of wastewater treatment plants, which has not been explored comprehensively. Finally, by leveraging C. vulgaris capabilities for carbon and nutrients sequestration, this study can provide practical guidance for achieving carbon neutrality in a WWTP.