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In the present paper, the feasibility of citrus wastewater treatment with aerobic granular sludge sequencing batch reactors (AGSBR) was investigated. Two AGSBRs (named R1 and R2, respectively) were operated for 90 days under different organic loading rates (OLR) and pH in two experimental periods. The OLR ranged approximately between 3.0 kg TCOD m−3d−1 and 7 kg TCOD m−3d−1 during Period I, whereas between 7 kg TCOD m−3d−1 and 15 kg TCOD m−3d−1 during Period II. pH was maintained at 7.0 and 5.5 in R1 and R2, respectively. The results revealed that under high OLR and unbalanced feast/famine regime (Period I), the development of fast-growing microorganisms (fungi and filamentous bacteria) was favoured in both reactors, resulting in granular sludge instability. An extended famine phase and a proper balancing between feast and famine periods (Period II) were favourable for the development of bacteria with low growth rates (0.05 d−1) thus enhancing the granules stability. To the benefit of granular sludge stability and effluent quality, the length of the feast period should not exceed 25% of cycle length. Moreover, under OLR lower than 7 kg TCOD m−3d−1 the removal efficiency of total chemical oxygen demand (TCOD) was approximately 90% in R1 and R2 and no side effects on the organic carbon removal performance related to the pH were observed. In contrast, at higher OLR a significant decrease in the removal efficiency (from 90% to less than 75%) was observed in R2. Results revealed also that under low pH, hydrolysis of proteins occurred and a decrease in the biological kinetic rates proportionally to the applied OLR was observed.