A laboratory-scale sequencing batch reactor (SBR) was operated for 450 days to assess aerobic granule formation when treating brewery/bottling plant wastewater by consistent application of a feast/famine regime. The experiment was divided into three major periods according to the different operational conditions: (I) no pH control and strong fluctuations in organic loading rate (OLR) (1.18 ± 0.25 kgCOD·(m3·day)−1), (II) pH control and aeration control strategy to reduce OLR fluctuations (1.45 ± 0.65 kgCOD·(m3·day)−1) and (III) no pH control and stable OLR (1.42 ± 0.18 kgCOD·(m3·day)−1). Aerobic granule formation was successful after 80 days and maintained during the subsequent 380 days. The aerobic granular sludge was characterized by SVI5 and SVI30 values below 60 mL.g−1 and dominated by granular, dense structures. An oxygen uptake rate based aeration control strategy insured endogenous respiration at the end of the aerobic phase, resulting in stable SBR operation when the influent composition fluctuated. The quantitative polymerase chain reaction results show no significant enrichment of Accumulibacter or Competibacter during the granulation process. The 16S rRNA sequencing results indicate enrichment of other, possibly important species during aerobic granule formation while treating brewery wastewaters.