The partial nitritation-anammox (PNA) process is the most promising technique to treat municipal sewage; however, nitrite oxidizing bacteria (NOB) are a hindrance to achieve PNA. This study investigated the effects of selectively discharging flocs (<200 μm) to washout NOB in a sequencing batch reactor (SBR) over 200 d. The experiment was divided into three phases with different floc sludge retention times (SRTs; 30, 20 and 30 d). When the SRT of the flocs was reduced from 30 to 20 d to washout NOB, a significant reduction of ammonia oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing (anammox) bacteria in the flocs was found. This indicates that a low floc SRT (20 d) leads to the loss of AOB and anammox bacteria in the flocs (<200 μm) and destroys PNA. Activity tests and qPCR analysis revealed the variations of functional bacteria in the granules and flocs, indicating that the enrichment of AOB, NOB, anammox bacteria in the granules is caused by the long-term discharging of flocs. High-throughput sequencing analysis revealed that the microbial shift of Tetrasphaera was significant in the flocs and may be connected to the enrichment of anammox bacteria and the stability of the PNA requires further research. All the obtained NOB sequences were affiliated with the genera Nitrospira and could further influence the PNA system. Overall, this study provides an in-depth understanding of the impact of discharging flocs to washout NOB and promotes the application of combing granules/floc PNA in sewage treatment. Display omitted •Controlling floc SRTs of 30 d was beneficial to stable operation of PNA.•Floc SRTs of 20 d would result in the reduction of AOB and Anammox in flocs.•The distribution of NOB in granules and flocs was impacted by long-term discharging flocs.•The microbial community structure was seriously affected by discharging flocs.