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This study presents a low-impact process that uses the synergy of peracetic acid (PAA) and graphene oxide quantum GQDs to degrade poorly biodegradable organic compounds and potentially substitute chlorination in wastewater treatment. The role of GQDs in GQDs/PAA activity and the effect of GQDs loading were examined. The results showed that increasing GQDs loading in the GQDs/PAA system greatly improved the photodegradation efficiency. Conversely, increasing the PAA concentration slightly enhanced efficiency due to few active sites being available. GQDs acted as catalysts and radical scavenging experiments confirmed that the degradation occurred via generation of hydroxyl (•OH) and peroxy (CH3C(=O)OO•)) radicals. A probable degradation mechanism of the organic dye was presented based on the reaction by-products detected after HPLC-MS studies. The E. coli inactivation mechanism was elucidated by monitoring the morphological changes of E. coli using scanning microscopy. The proposed antimicrobial mechanism includes the initial diffusion of PAA through the cell membrane which caused damage and induced cellular matter leakage, resulting in cell death. Bacterial regrowth studies confirmed GQDs/PAA were able to bypass the natural mechanisms of microorganisms that enables them to repair any damages in their DNA. [ABSTRACT FROM AUTHOR]