This study examines the effects of polyester and denim microfibers (MFs) on aerobic granular sludge (AGS) over a 42-day period. Treatment performance, granulation, and microbial community changes were assessed at 0, 10, 70, 210, and 1500 MFs/L. Reactors with 70 MFs/L achieved rapid granulation and showed improved settling by day 9, while 0 and 10 MFs/L reactors showed delayed granule formation, which was likely due to limited nucleation and weaker shear conditions. Severe clogging and frequent maintenance occurred at 1500 MFs/L. Despite > 98% MF removal in all reactors, treatment performance declined at higher MF loads. Nitrogen removal dropped from 93% to 68%. Phosphate removal slightly increased in reactors with no or low microfiber loads (96–99%), declined in reactors with 70 or 210 MFs/L (92–91%, 89–88%), and dropped significantly in the reactor with1500 MFs/L (86–70%, p < 0.05). COD removal declined with increasing MF load. Paracoccus (denitrifiers) dominated low-MF reactors; Acinetobacter (associated with complex organic degradation) and Nitrospira (nitrite-oxidizing genus) were enriched at 1500 MFs/L. Performance decline likely stemmed from nutrient transport blockage and toxic leachates, highlighting the potential threat of MFs to wastewater treatment and the need for upstream MF control.