The aim of this work was to analyze the changes in the emissions from the transport sector during the COVID-19 lockdown in Colombia. We compared estimated emissions from road transportation of four groups of pollutants, namely, greenhouse gases (CO2, CH4, N2O), ozone precursor gases (CO, NMVOC, NOx), aerosols (BC, PM2.5, PM10), and acidifying gases (NH3, SO2), during the first half of 2020 with values obtained in the same period of 2018. The estimate of emissions from road transportation was determined using a standardized methodology consistent with the 2006 Intergovernmental Panel on Climate Change (IPCC) Guidelines for National Greenhouse Gas Inventories and the European Environment Agency/European Monitoring and Evaluation Program. We found a substantial reduction in GHG emissions for CH4, N2O, and CO2 by 17%, 21%, and 28%, respectively. The ozone precursors CO and NMVOC presented a decrease of 21% and 22%, respectively, while NOx emissions were reduced up to 15% for the study period. In addition, BC decreased 15%, and there was a reduction of 17% for both PM10 and PM2.5 emissions. Finally, acidifying gases presented negative variations of 19% for SO2 and 23% for NH3 emissions. Furthermore, these results were consistent with the Ozone Monitoring Instrument (OMI) satellite observations and measurements at air quality stations. Our results suggest that the largest decreases were due to the reduction in the burning of gasoline and diesel oil from the transport sector during the COVID-19 lockdown. These results can serve decision makers in adopting strategies to improve air quality related to the analyzed sector.