Display omitted •Increasing the substrate concentration helped to improve the reactor tolerance.•In the P2 phase, side reactions impeded the removal of NO2–-N.•Filamentous bacteria, Ca and P synergistically promoted sludge granulation.•Anammox bacteria were reciprocal symbiosis with some heterotrophic bacteria. Most of the current studies have focused on the inhibition of anaerobic ammonium oxidation (anammox) by substrates, however, little attention has been paid to the recovery process of the reactor after inhibition. Therefore, we investigated the changes in reactor performance, granular sludge structure, and microbial community during the recovery phase after being inhibited by a high nitrogen load for 15 d. The nitrogen removal rate of the reactorwasrestored to pre-inhibition levels after 75 d of recovery, and the stoichiometric ratio converged to the theoretical value. The surface of the granular sludge developed into a broccoli-like structure, and the Ca and P contents of the granules increased from 6.88% and 4.39% to 24.42% and 13.88%, respectively. The abundance of the anammox bacterium Candidatus brocadia increased from 5.86% to 12.10%, and network analysis indicated that SMA102 and SBR1031 were positively correlated with the occurrence of Candidatus brocadia.