Emission factor and removal efficacy of PCNs are evaluated via the flue gas sampling of two MWIs equipped with different air pollution control devices (APCDs) in Taiwan. MWI-A is equipped with ESP, wet scrubber (WS) and selective catalytic reduction (SCR), while cyclone (CY), semi-dry absorber (SDA), activated carbon injection (ACI) and baghouse (BH) are employed in MWI-B. The average concentrations of PCNs measured at stacks of MWI-A and MWI-B are 2.1 ng Nm−3 (0.218 pg TEQ Nm−3) and 23.2 ng Nm−3 (0.425 pg TEQ Nm−3), respectively. The emission factors of PCNs calculated from feeding rates of waste and stack sampling results range from 6.7 to 6.95 μg t−1 (0.790–1.45 ng TEQ t−1). PCNs are formed in ESP via chlorination, while SCR and SDA + ACI + BH are effective in removing PCNs with the overall efficacies of 97.6% and 94.3%, respectively. PCN removal efficiencies achieved with SCR and SDA + ACI + BH increase as chlorination level increases. Specifically, around 72% and 82% of Mono-CN are removed by SCR and SDA + ACI + BH, respectively. The removal efficacies of other homologues achieved with SCR are consistently high (96–100%). Dominances of Mono-to Tri-CNs in scrubbing liquid collected from WS and higher removal efficacies of these homologues achieved with WS + ESP compared with ESP alone indicate that WS can capture low chlorinated PCNs to some extent. The results suggest that CY + SDA + ACI + BH should be equipped in MWI for effective removal of PCNs, while ESP, WS and SCR should be utilized with precaution to eliminate PCNs formation and enhance the PCNs removal efficiency.