Predicting the effects of the introduction of alternative transportation means on air quality is an important task for urban mobility planners. This study proposes a methodology that uses simulation to estimate the impact of changes in public transport on the traffic emissions of PM2.5. By using mobility planning information simulation models can be built, which can provide estimation of the dynamics of traffic over time. Then, coupling simulated traffic with emission factors of vehicles, an emission model can be used to estimate the total amount of PM2.5 emitted. With this approach, the effect of changes in the public transportation system can be assessed with respect to PM2.5 emissions. In the paper, we explore a case study in the city of Bogotá, Colombia, when a bus rapid transport system is to be added alongside a major city avenue.