Aerobic sludge granules are compact, strong microbial aggregates that have excellent settling ability and capability to efficiently treat high-strength and toxic wastewaters. The aerobic granules cultivated with low ammonium and phosphates lost structural stability within 3 days in continuous-flow reactors. Conversely, stable aerobic granules were cultivated in substrate with high levels of ammonium salts that could stably exist for 216 days in continuous-flow reactors with or without submerged membrane. The scanning electron microscopy, energy dispersive spectroscopy microanalysis and the confocal laser scanning microscopy imaging detected large amounts of calcium and iron precipitates in granule interiors. The Visual MINTEQ version 2.61 calculation showed that the phosphates and hydroxides were the main species in the precipitate.