This study elucidates the characteristics of persistent organic pollutants (POPs), including polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyl (PCBs), polybrominated dibenzo-p-dioxins and polybrominated dibenzofurans (PBDD/Fs) and polybrominated diphenyl ethers (PBDEs), that are emitted from a generator (non-road diesel engine) that is fueled with a blend of waste cooking oil biodiesels (WCO-biodiesels). Experimental results reveal that the mass concentrations of PCDD/Fs, PCBs, PBDD/Fs and PBDEs from the diesel generator that is fueled with petroleum diesel (D100) under loads of 1.5 kW and 3.0 kW were 583–875 pg Nm–3, 580–810 pg Nm–3, 982–1408 pg Nm–3, and 134–216 ng Nm–3, respectively, while the toxicity concentrations of PCDD/Fs, PCBs, and PBDD/Fs were 33.2–58.6, 2.72–3.11, and 1.54–2.30 pg WHO2005-TEQ Nm–3, respectively. W20 and W40 emitted 15–65% and 23–85% less of these POPs by mass (and 25–47% and 46–91% by toxicity), respectively. Among the tested fuel blends, the W40 exhibited the greatest emission factor reductions of mass and toxicity of these four POPs, despite of the load. Therefore, WCO-biodiesels can feasibly be used as an alternative generator fuel, favoring the recycling/reuse of waste oils and mitigating hazards to human health and environment.