Decarbonisation of a country’s energy system requires a change in energy supply chains, infrastructure and the introduction of new technologies. These lead to changes in the scale and type of combustion processes, the fuels used, as well as the activities required to supply fuels and operate energy infrastructure. They lead to changes in emission budgets of greenhouse gases and air pollutants that will have environmental and public health impacts. Such impacts can be highly dependent on the location and on the implementation of emerging energy technologies. This study compares the capabilities of tools for describing atmospheric emissions of air pollutants and greenhouse gases in future energy scenarios, for costing them and for cost-optimising deployment strategy. Case studies of technology choices for deploying decentralised CHP and for the uptake of hybrid vehicles are used to illustrate the challenges of representing emerging technologies in these models. The effectiveness of these technologies of reducing emissions budgets, together with synergies and antagonisms between delivering reductions in greenhouse gas emissions and air pollutant budgets are also explored. Recommendations are made on the using of incumbent models to assess air pollution, on the inclusion of novel technologies in energy scenarios and on how modelling systems might be better adapted to represent these. Spatial and temporal resolution are identified as key influences on models’ capabilities. In the hybrid vehicles case study, the precise technology options for vehicles – particularly hybrid powertrain architectures – is a key influence on optimising the benefits of atmospheric emissions reduction from future road transport. In the case of decentralised CHP, the surface morphology close to emission sources or in high population density areas will play a major role in impacts and costs of atmospheric emissions.