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Iron (Fe) phases are tightly linked to the preservation rather than the loss of organic carbon (OC) in soil; however, during redox fluctuations, OC may be lost due to Fe phase-mediated abiotic processes. This study examined the role of Fe phases in driving hydroxyl radical (•OH) formation and OC transformation during redox cycles in paddy soils. Chemical probes, sequential extraction, and Mössbauer analyses showed that the active Fe species, such as exchangeable and surface-bound Fe and Fe in low-crystalline minerals (e.g., green rust-like Fe phases), predominantly regulated •OH formation during redox cycles. The •OH oxidation strongly induced the oxidative transformation of OC, which accounted for 15.1–30.8% of CO2 production during oxygenation. Microbial processes contributed 7.3–12.1% of CO2 production, as estimated by chemical quenching and γ-irradiation experiments. After five redox cycles, 30.1–71.9% of the OC associated with active Fe species was released, whereas 5.2–7.1% was stabilized by high-crystalline Fe phases due to the irreversible transformation of these active Fe species during redox cycles. Collectively, our findings might unveil the under-appreciated role of active Fe phases in driving more loss than conservation of OC in soil redox fluctuation events.