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l Fast formation of micro-granules realized in a modified continuous-flow reactor. l Nitritation could be achieved within 6 days using the micro-granule (ca. 100 µm). l Maintaining ammonia in-excess was the key for NOB repression with micro-granules. l The micro-granules possessed ammonium oxidation potential of 59.3 ± 1.9 mg/g VSS/h. In this study, a modified continuous-flow nitrifying reactor was successfully operated for rapid cultivation of micro-granules and achieving robust nitritation. Results showed that sludge granulation with mean size of ca. 100 µm was achieved within three weeks by gradually increasing settling velocity-based selection pressure from 0.48 to 0.9 m/hr. Though Nitrospira like nitrite-oxidizing bacteria (NOB) were enriched in the micro-granules with a ratio between ammonia-oxidizing bacteria (AOB) and NOB of 5.7%/6.5% on day 21, fast nitritation was achieved within one-week by gradually increasing of influent ammonium concentration (from 50 to 200 mg/L). Maintaining ammonium in-excess was the key for repressing NOB in the micro-granules. Interestingly, when the influent ammonium concentration switched back to 50 mg/L still with the residual ammonium of 15–25 mg/L, the nitrite accumulation efficiency increased from 90% to 98%. Experimental results suggested that the NOB repression was intensified by both oxygen and nitrite unavailability in the inner layers of micro-granules. Unexpectedly, continuous operation with ammonium in excess resulted in overproduction of extracellular polysaccharides and overgrowth of some bacteria (e.g., Nitrosomonas, Arenimonas , and Flavobacterium), which deteriorated the micro-granule stability and drove the micro-granules aggregation into larger ones with irregular morphology. However, efficient nitritation was stably maintained with extremely high ammonium oxidation potential (> 50 mg/g VSS/hr) and nearly complete washout of NOB was obtained. This suggested that smooth and spherical granule was not a prerequisite for achieving NOB wash-out and maintaining effective nitritation in the granular reactor. Overall, the micro-granules exhibited a great practical potential for high-rate nitritation. Graphical Abstract [Display omitted]. [ABSTRACT FROM AUTHOR]