The energy sector is a major contributor to greenhouse gas (GHG) emissions and other types of air pollution that negatively impact human health and the environment. Policy targets to achieve decarbonisation goals for national energy systems will therefore impact levels of air pollution. Advantages can be gained from considering these co-impacts when analysing technology transition scenarios in order to avoid tension between climate change and air quality policies. We incorporated non-GHG air pollution into a bottom-up, technoeconomic energy systems model that is at the core of UK decarbonisation policy development. We then used this model to assess the co-impacts of decarbonisation on other types of air pollution and evaluated the extent to which transition pathways would be altered if these other pollutants were considered. In a scenario where the UK meets its existing decarbonisation targets to 2050, including the costs of non-GHG air pollution led to a 40% and 45% decrease in PM10 and PM2.5 pollution (respectively) between 2010 and 2050 due to changes in technology choice in residential heating. Conversely, limited change in the pollution profile for transportation were observed, suggesting that other policy strategies will be necessary to reduce pollution from transport.