•Colombia's on-road transportation emissions from 1990 to 2020 have been calculated.•Total transport emissions and trends have been compared with international sources.•High-resolution spatial distribution of transportation emissions has been computed. Road traffic-related air pollution costs society in terms of lost lives, health problems, and financial damages. For directing regulatory actions and enhancing air quality, governments require emission inventories and trends over time across all geographic areas. This study provides a high-resolution spatially disaggregated on-road transportation emissions inventory in Colombia from 1990 to 2020. Our estimates followed a top-down approach that accounted for local characteristics such as fleet technology, fuel consumption, road infrastructure, and activity factors at a national and state level. We report annual CO2, CH4, NOx, VOCs, PM2,5, and black carbon at a spatial resolution of 0.01° x 0.01°. Economic crises (1998–2001), stringent emission requirements (2011), and the most recent sanitary quarantine (2020) all have an impact on emissions patterns, which grow at a slower rate than vehicle activity. For the annual emissions of CH4, CO, and PM2.5, the growth of motorbikes in the vehicle fleet is particularly crucial.