A two-stage Partial Nitritation (PN)/Anammox process was carried out at lab-scale conditions to treat reject water from a municipal WWTP. PN was achieved in a granular SBR obtaining an effluent with a NH4+–N/NO2−–N molar ratio around 1.0. The microbial characterization of this reactor revealed a predominance of Betaproteobacteria, with a member of Nitrosomonas as the main autotrophic ammonium oxidizing bacterium (AOB). Nitrite oxidizing bacteria (NOB) were under the detection limit of 16S rRNA gene pyrosequencing, indicating their effective inhibition. The effluent of the PN reactor was fed to an Anammox SBR where stable operation was achieved with a NH4+–N:NO2−–N:NO3−–N stoichiometry of 1:1.25:0.14. The deviation to the theoretical stoichiometry could be attributed to the presence of heterotrophic biomass in the Anammox reactor (mainly members of Chlorobi and Chloroflexi). Planctomycetes accounted for 7% of the global community, being members of Brocadia (1.4% of the total abundance) the main anaerobic ammonium oxidizer detected. •Stable Partial Nitritation/Anammox treatment of sludge reject water yielded 88% of N removal.•The overall microbial community structure of both SBRs was analysed by 16S rRNA pyrosequencing.•In the nitritation reactor, Nitrosomonas were the main AOB while NOB were not detected.•Anammox activity was attributed to members of Brocadia accounting for 1.4% of the total community.