Vehicular emissions are a predominant source of pollution in urban environments. However, inherent complexities of vehicular behavior are sources of uncertainties in emission inventories (EIs). We compare bottom-up and top-down approaches for estimating road transport EIs in Manizales, Colombia. The EIs were estimated using a COPERT model, and results from both approaches were also compared with the official top-down EI (estimated from IVE methodology). The transportation model PTV-VISUM was used for obtaining specific activity information (traffic volumes, vehicular speed) in bottom-up estimation. Results from COPERT showed lower emissions from the top-down approach than from the bottom-up approach, mainly for NMVOC (−28%), PM10 (−26%), and CO (−23%). Comparisons showed that COPERT estimated lower emissions than IVE, with higher differences than 40% for species such as PM10, NOX, and CH4. Furthermore, the WRF–Chem model was used to test the sensitivity of CO, O3, PM10, and PM2.5 predictions to the different EIs evaluated. All studied pollutants exhibited a strong sensitivity to the emission factors implemented in EIs. The COPERT/top-down was the EI that produced more significant errors. This work shows the importance of performing bottom-up EI to reduce the uncertainty regarding top-down activity data.