Municipal solid waste (MSW) incinerators require effective flue gas treatment (FGT) to meet stringent environmental regulations. However, this in turn generates additional environmental costs through the impacts of materials and energy used in the treatment – these impacts are currently scarcely known. Therefore, this study uses life cycle assessment to estimate the impacts of different FGT systems typically found in modern MSW incinerators. A total of 12 scenarios are modelled to consider different combinations of the following eight technologies: electrostatic precipitators and fabric filters for removal of particulate matter; dry, semi-dry and wet scrubbers for acid gases; selective non-catalytic and catalytic reduction of nitrogen oxides (NOx); and activated carbon for removal of dioxins and heavy metals. The data are sourced from 90 full-scale incinerators operating in France. The results reveal that a dry system using sodium bicarbonate and selective non-catalytic reduction (SNCR) is the best option for seven out of 18 impacts, including climate change (37.1 kg CO2 eq./t MSW). By contrast, a dry system with calcium hydroxide and selective catalytic reduction (SCR) has the highest impacts in six categories, including climate change (102 kg CO2 eq./t MSW). The wet systems have higher impacts than the dry alternatives, with the semi-dry options being in between. Compared to SNCR, the use of SCR decreases the NOx-related impacts (fine particulate matter formation, terrestrial acidification and photochemical ozone formation) but increases other impacts. For example, the SCR systems have 49–284% greater climate change and 43–150% higher depletion of fossil resources than their SNCR counterparts. Overall, all FGT systems reduce significantly fine particulate matter formation (by 81–88%), photochemical ozone formation (76–90%) and terrestrial acidification (83–90%). However, they also cause 14 other impacts which would not be generated if the flue gas was left untreated, thus creating additional environmental costs. These include climate change, resource depletion and human and ecotoxicities. Therefore, these trade-offs should be considered carefully to minimise the unintended environmental consequences of flue gas treatment from incineration of MSW.