Achieving mainstream nitritation with aerobic granules is attractive based on increasing evidence but generally treating artificial low-ammonium wastewater. Real municipal wastewater is much more complex in composition, the behavior of the nitritation granules would be different when treating real municipal wastewater. Herein, the response of nitritation granules to influent shift from artificial low-ammonium (35–40 mg/L) wastewater to anaerobically pre-treated municipal wastewater (MWW pre-treated) was investigated at low temperatures. Results showed that MWW pre-treated caused the outgrowth of filamentous bacteria on the granule surface and developed into finger-like structures, which in turn resulted in the decrease of the overall granular sludge settleability. Batch-tests and microbial analysis indicated the functional and microbial differentiation between the newly formed fluffy exterior and the original compact granule. The fluffy exterior was dominated by genus Flavobacterium (66.6%) and primarily functioned as COD removal, whereas the nitrifiers (mainly Nitrosomonas) were still located in the compact core and performed nitritation. Moreover, the heterotrophs-dominated fluffy exterior hindered the oxygen transfer towards nitrifiers located in the compact granule and thereby facilitated the stable NOB repression in the granule particularly at low temperatures (<10 °C). Finally, gradual recovery of the granular sludge morphology and settleability occurred after the influent reverted to synthetic low-ammonium wastewater. Overall, this work demonstrated that the feeding of MWW pre-treated only caused morphological changes of the nitritation granules, but its structural and functional stability could be maintained stably. [Display omitted] • Granule-based nitritation was maintained treating anaerobically pretreated sewage. • COD removal occurred primarily in external flocs, while nitritation in compact core. • External flocs promoted NOB repression by increasing oxygen transfer resistance. [ABSTRACT FROM AUTHOR]