This study quantifies the hydraulic performance of a pilot-scale ultrafiltration system integrated into a full-scale industrial aerobic granular sludge (AGS) plant. The treatment plant consisted of parallel AGS reactors, Bio1 and Bio2, with similar initial granular sludge properties. During the 3-month filtration test, a chemical oxygen demand (COD) overloading episode took place, affecting the settling properties, morphology, and microbial community composition in both reactors. The impact on Bio2 was more severe than on Bio1, with higher maximal sludge volume index values, a complete loss of granulation, and the excessive appearance of filamentous bacteria extending from the flocs. The membrane filtration properties of both sludges, with these different sludge qualities, were compared. The permeability in Bio1 varied between 190.8 ± 23.3 and 158.9 ± 19.2 L·m-2·h-1·bar-1, which was 50% higher than in Bio2 (89.9 ± 5.8 L·m-2·h-1·bar-1). A lab-scale filtration experiment using a flux-step protocol showed a lower fouling rate for Bio1 in comparison with Bio2. The membrane resistance due to pore blocking was three times higher in Bio2 than in Bio1. This study shows the positive impact of granular biomass on the long-term membrane filtration properties and stresses the importance of granular sludge stability during reactor operation.