Fossil fuels in transportation are a significant source of local emissions in and around cities; thus, decarbonising transportation can reduce both greenhouse gases (GHGs) and air pollutants (APs). However, the degree of these reductions depends on what replaces fossil fuels. Today, GHG and AP mitigation strategies are typically ‘decoupled’ as they have different motivations and responsibilities. This study investigates the ancillary benefits on (a) APs if the transport sector is decarbonised, and (b) GHGs if APs are drastically cut and (c) the possible co-benefits from targeting APs and GHGs in parallel, using an energy-system optimisation model with a detailed and consistent representation of technology and fuel choices. While biofuels are the most cost-efficient option for meeting ambitious climate-change-mitigation targets, they have a very limited effect on reducing APs. Single-handed deep cuts in APs require a shift to zero-emission battery electric and hydrogen fuel cell vehicles (BEVs, HFCVs), which can result in significant upstream GHG emissions from electricity and hydrogen production. BEVs powered by ‘green’ electricity are identified as the most cost-efficient option for substantially cutting both GHGs and APs. A firm understanding of these empirical relationships is needed to support comprehensive mitigation strategies that tackle the range of sustainability challenges facing cities.