To assess the stability of aerobic granular sludge (AGS) under nitrogen deficiency conditions, three sequence batch reactors were operated with chemical oxygen demand (COD) to nitrogen (N) ratios of 100/5, 100/2.5, and 100/2, while COD concentration was kept consistent. AGS variations in its physicochemical characteristics, microbial community, and treatment performance were investigated. The results indicated that good treatment performance and stable AGS were achieved under nitrogen deficiency. Extracellular polymeric substances (EPS) regulating mechanism preserved AGS stability under nitrogen deficiency, especially through increased secretion of polysaccharide. In addition, members of the Anaerolineaceae were the major filamentous bacteria, which are strictly anaerobic organism, providing a possible explanation to the lack of filamentous bacteria outgrowth under N deficient condition. Insights from this study could help lower chemical costs in AGS applications for specific industrial wastewater treatments.