Abstract • PN-A was start-up under low inoculation amount and a higher NRR was achieved. • PN-anammox system was successfully restored by aggressive sludge discharge. • Increase in granular sludge was the important factor to rapid recovery. • Enrichment of AOB and AnAOB in granular sludge favors the stable operation. Partial nitritation (PN)-anaerobic ammonium oxidation (anammox) is a promising pathway for the biological treatment of wastewater. However, the destruction of the system caused by excessive accumulation of nitrate in long-term operation remains a challenge. In this study, PN-anammox was initialized with low inoculation quantity in an air-lift reactor. The nitrogen removal rate of 0.71 kgN/(m3·d) was obtained, which was far higher than the seed sludge (0.3 kgN/(m3·d)). Thereafter, excess nitrate build-up was observed under low-loading conditions, and recovery strategies for the PN-anammox system were investigated. Experimental results suggest that increasing the nitrogen loading rate as well as the concentration of free ammonium failed to effectively suppress the nitrite oxidation bacteria (NOB) after the PN-anammox system was disrupted. Afterwards, effluent back-flow was added into the reactor to control the up-flow velocity. As a result, an aggressive discharge of sludge that promoted the synergetic growth of functional bacteria was achieved, leading to the successful restoration of the PN-anammox system. The partial nitritation and anammox activity were in balance, and an increase in nitrogen removal rate up to 1.07 kgN/(m3·d) was obtained with a nitrogen removal efficiency of 82.4% after recovery. Besides, the proportion of granular sludge (over 200 mm) increased from 33.67% to 82.82%. Ammonium oxidation bacteria (AOB) along with anammox bacteria were enriched in the granular sludge during the recovery period, which was crucial for the recovery and stable operation of the PN-anammox system.