This study aimed at assessing the performance and microbial community in a granular one-stage partial nitritation-anammox sequencing batch reactor (PNA-SBR) subjected to temperature transition from 25 to 15 °C without biomass acclimation. The PNA-SBR was operated by controlling the oxygen transfer rate (OTR) according to the ammonium loading rate (ALR), which resulted in micromolar (µM) bulk dissolved oxygen (DO) concentration. The applied strategy proved to be feasible to operate the one-stage PNA-SBR at mainstream conditions because it was possible to control nitritation according to anammox rate. Nitrogen removal rate (NRR) of 330.24 ± 25.36 mg N·L−1·d−1 was achieved at 25 °C. Nitratation control by µM bulk DO limited the NO3 − production:NH4 + removed at 0.28 ± 0.04. No instability was experienced by decreasing the temperature to 15 °C, but removal rates were adapted to the resulting anammox activity, which decreased at low temperature. After temperature transition, nitratation was kept controlled and the NO3− production:NH4 + removed molar ratio remained at 0.33 ± 0.05, although anammox activity deteriorated and higher nitrate production was obtained. Sequencing analysis revealed the dominant bacterial groups in the microbial community that clustered within the phyla Planctomycetes, Proteobacteria, Chloroflexi, and Bacteroidetes. Temperature drop only affected bacterial abundance, but the main bacteria involved in nitrification and anammox processes did not change during the study. Candidatus Kuenenia was the main anammox genus. Moreover, the presence of bacterial groups associated with heterotrophic metabolism indicates denitrification might be supported by the release of dissolved organic carbon due to bacterial lysis, and lower nitrate effluent concentration could be reached in PNA reactors.