An electro-Fe2+-activated peracetic acid (EC/Fe2+/PAA) process was established for organic dye removal in water. The operation factors such as the PAA dosage, Fe2+ amount, current density, and pH were investigated on methylene blue (MB) removal for the synergistic EC/Fe2+/PAA system. Efficient MB decolorization (98.97% and 0.06992 min−1) was achieved within 30 min under 5.4 mmol L−1 PAA, 30 μmol L−1 Fe2+, 15 mA cm−2 current intensity, and pH 2.9. Masking tests affirmed that the dominating radicals were hydroxyl radicals (OH), organic radicals (CH3CO2·, CH3CO3·), and singlet oxygen (1O2), which were generated from the activated PAA by the synergetic effect of EC and Fe2+. The influence of inorganic ions and natural organic matter on the MB removal was determined. Moreover, the efficacy of the EC/Fe2+/PAA was confirmed by decontaminating other organic pollutants, such as antibiotic tetracycline and metronidazole. The studied synergy process offers a novel, advanced oxidation method for PAA activation and organic wastewater treatment.