An assessment was performed for elucidating the possible impact of different aeration strategies on the carbon footprint of a full-scale wastewater treatment plant. Using a calibrated model, the impact of different aeration strategies was simulated. The ammonia controller tested showed its ability in ensuring effluent ammonia concentrations compliant with regulation along with significant savings on aeration energy, compared to fixed oxygen set point (DOsp) control strategies. At the same time, nitrous oxide emissions increased due to accumulation of nitrification intermediates. Nevertheless, when coupled with the carbon dioxide emissions due to electrical energy consumption for aeration, the overall carbon footprint was only marginally affected. Using the local average CO2 emission factor, ammonia control slightly reduced the carbon footprint with respect to the scenario where DOsp was fixed at 2 mg·L−1. Conversely, no significant change could be detected when compared against the scenarios where the DOsp was fixed. Overall, the actual impact of ammonia control on the carbon footprint compared to other aeration strategies was found to be strictly connected to the sources of energy employed, where the larger amount of low CO2-emitting energy is, the higher the relative increase in the carbon footprint will be.