It has been widely accepted that iron plays an important role in stimulating the activity of anammox bacteria, which contain many iron clusters for electron transport in cells. However, whether anammox bacteria could directly use and how to uptake Fe(III) have been long-time ignored. Here, we found that micrometer-scale magnetite with the size of 10–20 μm significantly promoted the anammox bacterial activity by iron core and iron uptake. Anammox bacteria cannot utilize Fe(III) directly as they are unable to secrete siderophore for the extracellular Fe(III) transfer to intracellular. In anaerobic anammox consortia at the presence of magnetite, siderophore synthesis bacteria belonging to Alphaproteobacteria, Candidate phylum, and Chloroflexi secreted abundant siderophores, which combined with Fe(III) ionized from magnetite to form siderophore-Fe(III) complexes. These complexes were then used by anammox bacteria via a specific outer membrane receptor and transported by the transporter protein to the periplasm, further releasing Fe(III). Cytochrome c was then formed by the siderophore-Fe(III) complex reduction, for assimilation and synthesis of Fe–S protein and heme B in anammox bacteria to increase electron transfer capability. This study reveals the siderophore-mediated bacterial cooperation in anammox consortia for Fe(III) assimilation and implies the important role of siderophore-mediated cooperation in driving nitrogen conversion in the artificial or natural system.