Retarding the fuel injection timing is an effective strategy for controlling NOx emissions from diesel engines. However, the influence of retarding the fuel injection timing on polycyclic aromatic hydrocarbon (PAH) and persistent organic pollutant (POP) emissions has not yet been investigated. In this study, the diesel engine was tested using four of the existing thirteen European steady state cycle (ESC) modes. The fuel injection timing was retarded from –8° to –6° and the diesel exhaust gas samples were analyzed for PAH and POP emissions. The NOx emission factor reduced by ~25% when the fuel injection timing was retarded. However, the strategy had a negative effect on combustion efficiency. The carbon monoxide (CO) and particulate matter (PM) emissions were 1.4 and 1.2 times higher for the –6° scenario, respectively. The emission factors of all the toxic organic pollutants increased drastically when the fuel injection timing was retarded. For instance, the emission factors of PAH and polychlorinated dibenzo-p-dioxin/dibenzofuran (PCDD/F) for the –6° scenario, based on BaPeq and WHO-TEQ, were 22 and 10 times higher than for the –8° scenario. The retardation had more influence on these pollutants in the particle-phase than in gas-phase. The resultant negative impact on combustion increased the emissions of products of incomplete combustion, enhancing the potential of POP formation via de novo synthesis. The study concludes that although retarding the fuel injection timing leads to a decrease in NOx emissions from diesel engines, it also results in an increase in PAH and POP emissions.