The formation and evolution of aerobic granular sludge (AGS) developed in a sequential batch reactor (SBR) were evaluated to understand the effect of influential operating parameters on its morphology, stability, and removal performance while treating industrial/municipal wastewater. After 18 days of operation (stage I), mature granules were identified in the reactor, and in 25 days, the AGS system reached a stable operation. The chemical oxygen demand (COD) and total Kjeldahl nitrogen (TKN) were affected by the applied operating variations (from stages II to VII). Until day 48 (stage III), the aerobic granules did not show relevant changes in shape and stability. During this stage, the AGS system achieved high removal efficiencies of COD (97.7%) and TKN (86.2%) and a sludge volume index (SVI) of 65 ± 6.7 mL/g-total suspended solids. From stage IV until the end of the reactor operation, partial disintegration and rupture occurred in the system, but granules did not completely disintegrate. Specifically, a volumetric exchange ratio (VER) of >67% and an aeration rate (AR) of <2.5 L/min promoted the compactness and the structural integrity of AGS. The principal component analysis corroborated that the rise in the VER is an effective strategy for improving AGS stability and organic pollutant removal.