This work aimed to compare the carbon footprint (CF) of six full-scale wastewater treatment plants (WWTPs). The CF was estimated in the range of 23-100 kg CO per population equivalent. In the total CF, the direct emissions held the highest share (62-74%) for the plants with energy recovery from biogas. In the plants depending entirely on the power grid, the indirect emissions due to energy consumption dominated the total CF (69-72%). The estimated CF was found highly sensitive towards the choice of NO emission factors. A dual effect of external substrates co-digestion on the CF has been presented. After co-digestion, the overall CF decreased by 7% while increasing the biogas production by 17%. While applying the empirical model, the level of energy neutrality was strongly related to the ratio of the indirect to direct emissions.