On-road traffic is the primary source of air pollutants in Cuenca (2500 m. a.s.l.), an Andean city in Ecuador. Most of the buses in the country run on diesel, emitting high amounts of NOx (NO + NO2) and PM2.5, among other air pollutants. Currently, an electric tram system is beginning to operate in this city, accompanied by new routes for urban buses, changing the spatial distribution of the city’s emissions, and alleviating the impact in the historic center. The Ecuadorian energy efficiency law requires that all vehicles incorporated into the public transportation system must be electric by 2025. As an early and preliminary assessment of the impact of this shift, we simulated the air quality during two scenarios: (1) A reference scenario corresponding to buses running on diesel (DB) and (2) the future scenario with electric buses (EB). We used the Eulerian Weather Research and Forecasting with Chemistry (WRF-Chem) model for simulating the air quality during September, based on the last available emission inventory (year 2014). The difference in the results of the two scenarios (DB-EB) showed decreases in the daily maximum hourly NO2 (between 0.8 to 16.4 µg m−3, median 7.1 µg m−3), and in the 24-h mean PM2.5 (0.2 to 1.8 µg m−3, median 0.9 µg m−3) concentrations. However, the daily maximum 8-h mean ozone (O3) increased (1.1 to 8.0 µg m−3, median 3.5 µg m−3). Apart from the primary air quality benefits acquired due to decreases in NO2 and PM2.5 levels, and owing to the volatile organic compounds (VOC)-limited regime for O3 production in this city, modeling suggests that VOC controls should accompany future NOx reduction for avoiding increases in O3. Modeled tendencies of these pollutants when moving from the DB to EB scenario were consistent with the tendencies observed during the COVID-19 lockdown in this city, which is a unique reference for appreciating the potentiality and identifying insights for air quality improvements. This consistency supports the approach and results of this contribution, which provides early insights into the effects on air quality due to the recent operability of the electric tram and the future shift from diesel to electric buses in Cuenca.