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BACKGROUND Three lab‐scale sequencing batch reactors were used to investigate the effects of Fe3+ on aerobic granular sludge (AGS) formation, nutrient removal, and microbial community. RESULTS The addition of 6 and 12 mg Fe3+ L−1 could not shorten the granulation time. However, compared to the reactor without Fe3+ addition (average sludge volume index at 30 min (SVI30) 70.8 mL g−1; stable average particle size 548 μm), the addition of 12 mg Fe3+ L−1 helped improve the physical properties of AGS (average SVI30 57.0 mL g−1; stable average particle size 1067 μm). Furthermore, with 12 mg Fe3+ L−1 addition (Fe3+ to PO43−‐P molar ratio = 1.33), effective removal of NH4+‐N (≤0.5 mg L−1) and PO43−‐P (<1 mg L−1) was achieved. The addition of Fe3+ reduced the microbial diversity and specific activity of heterotrophic bacteria, but promoted the growth of nitrite‐oxidizing bacteria. The growth of particle size not only increased the active biomass ratio and microbial diversity, but alleviated the inhibition effect of Fe3+ on the specific heterotrophic bacteria activity. CONCLUSION The addition of Fe3+ had both negative and positive effects on the formation and stability of AGS. The results will help enrich the understanding of AGS application in nutrient removal and especially that of phosphorus. © 2020 Society of Chemical Industry