Aerobic granular sludge (AGS) technology holds great promise of becoming the standard for biological wastewater treatment due to its lower energy consumption, small footprint, and high removal efficiency of nutrients compared to the conventional activated sludge processes. Different-sized aggregates have been shown to harbor a different microbial community composition. The central question is do full-scale AGS wastewater treatment plants (WWTPs) select for core microbial communities across different aggregate sizes and how these selected organisms differ between the different-sized aggregates. This study analyzed samples from nine geographically distributed full-scale AGS WWTPs that consistently perform well in terms of chemical oxygen demand (COD) and nutrient (N and P) removal. The main results showed that site-specific conditions highly influence microbial composition in smaller aggregates (< 1 mm), while larger granules form stable communities independent of WWTP location. Notably, all aggregates contained a small subset of 128–139 core OTUs that were both prevalent and abundant across all sizes. These core OTUs include key functional groups such as fermenters, aerobic heterotrophs, polyphosphate-accumulating organisms (PAOs), glycogen-accumulating organisms (GAOs), and nitrifiers, which play a crucial role in COD and nutrient removal. Additionally, an enrichment pattern was observed, with aerobic heterotrophs dominating in flocs, PAOs in small granules, and GAOs and nitrifiers in large granules. This study offers valuable insights into the core microbiome of different-sized aggregates in full-scale AGS WWTPs and highlights their potential role in overall system performance.