This study investigates fine particulate matter (PM2.5) bound persistent organic pollutants (POPs) emitted from a diesel generator fueled with three waste cooking oil-based biodiesel (WCO-biodiesel) blends (W0 (pure diesel), W20 (WCO-biodiesel/diesel = 20%/80% (v/v)), and W40). These POPs are polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyl (PCBs), polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/Fs) and polybrominated diphenyl ethers (PBDEs). Experimental results indicate that the mass concentrations of PM2.5-bound PCDD/Fs, PCBs, PBDD/Fs and PBDEs in the engine exhaust are 2.15–3.65, 16.7–35.4, 25.8–46.5 and 303–440 pg Nm–3, respectively, at 1.5–3.0 kW loads for using W0, while the corresponding toxic equivalent (TEQ) concentrations of the above PM2.5-bound pollutants are 0.282–0.527, 0.038–0.051 and 0.064–0.093 pg WHO2005-TEQ Nm–3, respectively (excluding PBDEs, which still have no toxic equivalency factors (TEFs) for TEQ calculation). Using W20 and W40 reduced the mass and TEQ emission concentrations of PM2.5-bound PCDD/Fs, PCBs, PBDD/Fs and PBDEs in comparison with W0. The reductions of mass concentrations in exhausted PM2.5 were in the order PBDEs >> PBDD/Fs > PCBs > PCDD/Fs, while the decrease in toxic concentration followed the order PCDD/Fs > PBDD/Fs > PCBs. Thus, adding WCO-biodiesel to the fuel mixture in generator engines lowers the adverse effects of PM2.5 emissions on the environment and human health.