<p>The limited iron uptake efficiency of anaerobic ammonium oxidation (anammox) bacteria has garnered accumulating concerns, as iron plays an important role in anammox bacteria metabolism. Siderophores are a prevalent strategy for iron acquisition among many bacteria, and recent evidence has suggested the potential role of siderophore-Fe³⁺ as bioavailable iron sources to anammox bacteria. Nonetheless, what target siderophore anammox bacteria can use and how they use it remain poorly understood. Here we shed fresh light on siderophore selectively promoting iron uptake and regulating the metabolic activity of anammox bacteria. Batch experiments and long-term operations demonstrated that siderophores catechin (CAT) and <i>N</i>-hydroxyethyl ethylenediamine triacetic acid (HEDTA) increased the iron uptake efficiency of anammox consortia up to 50%–65% and triggered the cofactors synthesis for key enzymes assembly, thereby selectively enhancing the anammox activity (≥350 mg N per gram of volatile suspended solids per day) and nitrogen removal efficiency (≥85%). Integrated with multi-omics approaches, we revealed versatile iron uptake pathways within anammox bacteria genera: <i>Candidatus</i> Brocadia acquired CAT-Fe³⁺ and HEDTA-Fe³⁺ via outer membrane receptors FitA/TbpA and FecA, respectively, whereas <i>Candidatus</i> Jettenia initially reduced CAT-Fe³⁺ using NfnB enzyme before uptake via the FeoABC system. This work reveals a pivotal role of siderophores in selectively enhancing anammox bacteria by optimizing their iron uptake and utilization and uncovers the involved molecular mechanisms, which opens promising avenues to optimize the anammox process with siderophore regulation for more efficient and sustainable wastewater treatment.</p>