Coupling a traffic microsimulation with an emission model is a means of assessing fuel consumptions and pollutant emissions at the urban scale. Dealing with congested states requires the efficient capture of traffic dynamics and their conditioning for the emission model. Two emission models are investigated here: COPERT IV and PHEM v11. Emission calculations were performed at road segments over 6 min periods for an area of Paris covering 3 km2. The resulting network fuel consumption (FC) and nitrogen oxide (NOx) emissions are then compared. This article investigates: (i) the sensitivity of COPERT to the mean speed definition, and (ii) how COPERT emission functions can be adapted to cope with vehicle dynamics related to congestion. In addition, emissions are evaluated using detailed traffic output (vehicle trajectories) paired with the instantaneous emission model, PHEM. COPERT emissions are very sensitive to mean speed definition. Using a degraded speed definition leads to an underestimation ranging from -13% to -25% for fuel consumption during congested periods (from -17% to -36% respectively for NOx emissions). Including speed distribution with COPERT leads to higher emissions, especially under congested conditions (+13% for FC and +16% for NOx). Finally, both these implementations are compared to the instantaneous modeling chain results. Performance indicators are introduced to quantify the sensitivity of the coupling to traffic dynamics. Using speed distributions, performance indicators are more or less doubled compared to traditional implementation, but remain lower than when relying on trajectories paired with the PHEM emission model.