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We hereby report the synthesis, characterization, and computational analysis of novel bimetallic PdRu nanoparticles (PdRuNPs) using the quercetin-para aminobenzoic acid (QPABA) ligand and their application in developing a sensitive and scalable electrochemical system for effective detection and degradation of 1,4-dioxane in water samples. The fabricated nanocatalysts were subjected to UV–visible spectroscopy, particle size analyzer, XRD, SEM, STEM–EDX, TEM, and FTIR. Also, the DFT B3LYP computational study shows that stable PdRuNPs form through Pd and Ru interactions with QPABA at the carboxyl OH sites on the G and F rings, respectively. The limit of detection for 1,4-dioxane was determined to be 0.034 ppb, which is below the U.S. Environmental Protection Agency’s advisory range. Additionally, combining liquid–liquid extraction with GC–MS for the detection of 1,4-dioxane registered a method detection limit of 0.033 ppb in real wastewater samples. In the scaled-up system, three actual wastewaters from a wastewater treatment plant in New Jersey containing 1,4-dioxane up to 300 ppm were able to be 100% removed within 30 min. In addition, LC–MS analysis revealed the final reduction of 1,4-dioxane to carbon dioxide and water. This study provides a reliable method for the scalable and simultaneous detection and degradation of hazardous chemicals, enhancing the environmental safety.