This investigation focuses on the effects on emissions of persistent organic pollutants (POPs) (polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs), polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/Fs) and polybrominated diphenyl ethers (PBDEs)) from a diesel engine fuelled by 20 vol% waste cooking oil-based biodiesel (W20) blended with various fractions of dehydrate/hydrous butanol (B/B′) and acetone (A/A′). The emission concentrations of the POPs were in the order PBDE ≫ PBDD/F > PCB > PCDD/F, regardless of the blending fuel or engine load. The POP with highest concentration was PBDE, being 2–3 times that of the others. Conversely, the magnitude of emitted toxicity followed the order PCDD/F > PCB ≈ PBDD/F, while PCDD/F emissions had about 10 times the toxicity concentrations of PCBs and PBDD/Fs. Among the dioxin compounds, the emissions of PCDDs represented 46–73% (average 57%) and 50–72% (average 59%) of total PCDD/F mass and toxicity concentrations, respectively, and were which and were thus significantly higher than those of PCDFs. The non-ortho-PCB contributed almost all toxicity (~100%) of 14 dioxin-like-PCBs, even though its contribution in mass was only 9–32% (average 16%) among the congeners. Similarly, PBDFs accounted for ~100% of toxicity of PBDD/Fs. Additionally, deca-BDEs contributed to most of the mass emissions of PBDEs (47.0–90.5%, 82.4% in average), while nona-BDEs and tri- to octa-BDEs only contributed 10% and 8%, respectively. The reductions of the absolute mass concentrations of POPs from W20 were in the order PBDEs >> PBDD/Fs > PCDD/Fs ≈ PCBs for all multi-component diesel blends. The reduction fractions of POPs were in the order PCDD/F > PCB ≈ PBDD/F > PBDE, and those of TEQ were PCDD/F > PCB > PBDD/F. Thus, the addition of butanol and acetone, whether pure or hydrous, could further lower the POP emissions from W20.