The chronic effects of titanium dioxide nanoparticles (TiO2 NPs) on aerobic granular sludge (AGS) and algal–bacterial granular sludge (ABGS) was examined in this study. Sequencing batch bioreactors (SBRs) and photo sequencing batch bioreactors (PSBRs) were operated with synthetic wastewater containing 0, 1, 5, 10, 20, 30, and 50 mg L−1 TiO2 NPs for 10 days. Nanoparticles at concentrations of 1 and 5 mg L−1 did not impact nutrient removal but led to an increase in extracellular polymeric substances (EPSs), primarily in protein (PN). With increasing nanoparticle concentration, the negative effect became more pronounced, mainly in the AGS SBRs. At 50 mg L−1 TiO2, chemical oxygen demand (COD), ammonia–nitrogen (NH3-N), and phosphorus (PO43−) removal decreased by 20.9%, 12.2%, and 35.1% in AGS, respectively, while in ABGS, they reached only 13.4%, 5.7%, and 14.2%. ABGS exhibited steady-state nutrient removal at 30 and 50 mg L−1 TiO2 NPs after around 5 days. The higher microbial activity and EPS content in the sludge, coupled with the symbiotic relationship between algae and bacteria, contributed to the higher tolerance of ABGS to nanoparticles. Finally, although nanoparticles reduced biomass in both types of bioreactors, the accumulation of TiO2 NPs in the sludge, confirmed by Energy-dispersive X-ray spectroscopy analysis, and the absence of detectable titanium concentrations in the effluent wastewater, measured by Inductively-coupled plasma mass spectrometry, may be attributed to the specific operational conditions of this study, including the relatively short operation period (10 days) and high initial MLSS concentration (6 g L−1).