The transformations of carbon, nitrogen, and iron are closely interrelated within the elemental biogeochemical cycles, influenced by numerous factors. The key roles of Shewanella in the three cycles, which drives Biological Fenton (Bio-Fenton) and improves biological nitrogen removal, have not been clarified. In this study, by coupling Anammox with Bio-Fenton in the cathodic chamber of a microbial electrochemical system (MES), we explored the ability of Shewanella to force C, N, and Fe transformation, and excavated the interactions among the complex reactions. In the coupling systems, nitrogen removal efficiency was enhanced by 22.69%, and Shewanella-mediated Fe (III) reduction improved hydroxyl radical (OH) production to decompose 1,4-dioxane. Fe (II) was generated with electrons from the cathode and then chemically oxidized, and one-electron transfer pathway was prioritized in OH production. Functional gene abundance reflected that the antioxidant systems of microorganisms were highly developed to resist the oxidative stress. The robustness of the coupling systems was demonstrated during long-term operation. This study provides valuable insights into the importance of Shewanella in redox zones and presents novel technological advancements for wastewater treatment.