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Nitrous oxide, carbon dioxide and methane are greenhouse gases (GHG) emitted from wastewater treatment that contribute to its carbon footprint. As a result of the increasing awareness of GHG emissions from wastewater treatment plants (WWTPs), new modelling, design, and operational tools have been developed to address and reduce GHG emissions at the plant-wide scale and beyond. This paper reviews the state-of-the-art and the recently developed tools used to understand and manage GHG emissions from WWTPs, and discusses open problems and research gaps. The literature review reveals that knowledge on the processes related to N2O formation, especially due to autotrophic biomass, is still incomplete. The literature review shows also that a plant-wide modelling approach that includes GHG is the best option for the understanding how to reduce the carbon footprint of WWTPs. Indeed, several studies have confirmed that a wide vision of the WWPTs has to be considered in order to make them more sustainable as possible. Mechanistic dynamic models were demonstrated as the most comprehensive and reliable tools for GHG assessment. Very few plant-wide GHG modelling studies have been applied to real WWTPs due to the huge difficulties related to data availability and the model complexity. For further improvement in GHG plant-wide modelling and to favour its use at large real scale, knowledge of the mechanisms involved in GHG formation and release, and data acquisition must be enhanced.