The motivation for conducting this research stems from the increasingly applied manipulations of emission control systems (ECSs), especially those in diesel passenger cars (PCs). The study aimed to investigate the influence of manipulations of exhaust gas recirculation (EGR) valves and a diesel exhaust fluid (DEF)-dosing system on the nitrogen oxide (NO_X) emissions of a Euro 6 diesel vehicle and, through the quantification of vehicles with manipulated ECSs, estimate the emissions of Euro 6 diesel PCs. Portable emissions measurement system (PEMS) measurements were performed on a Euro 6 diesel vehicle at a constant speed and on real driving emission (RDE) routes. The speed-dependent functions of the NO_X hot emission factor (EF) were calculated for seven different scenarios. The results showed that the NO_X EFs for the worst-case scenarios were more than two orders of magnitude higher than those where all ECSs were active. Applying the calculated EFs and the survey answers on the percentage of manipulated PCs to the Croatian Euro 6 diesel PC fleet, the results showed that the emission levels were up to 46.3% higher than the emissions calculated by the official computer program COPERT v5.6.5, with a tendency towards significantly higher values. The main conclusion is that vehicle manufacturers, policymakers, and the general public need to be informed about the enormous damage that in-use vehicles with manipulated ECSs cause to the environment and human health, in order to prevent such actions.