To understand the long-term stability of nitrifying granules in a membrane bioreactor (GMBR), a membrane module was submerged in an airlift reactor to eliminate the hydraulic selection pressure that was believed to be the driving force of aerobic granulation. The long-term monitoring results showed that the structure of nitrifying granules could remain stable for 305 days in the GMBR without hydraulic selection pressure; however, the majority of the granule structure was actually inactive due to mass diffusion limitation. As a consequence, active biomass free of mass diffusion limitation only inhabited the top 60–80 µm layer of the nitrifying granules. There was a dynamic equilibrium between bioflocs and membrane, i.e., 25% of bioflocs attached on the membrane surface within the last nine days of the backwash cycle in synchronization with the emergence of a peak of soluble extracellular polymeric substances (sEPS), with a concentration of around 47 mg L−1. Backwash can eventually detach and return these bioflocs to the bulk solution. However, the rate of membrane fouling did not change with and without the biofloc attachment. In a certain sense, the GMBR investigated in this study functioned in a similar fashion as an integrated fixed-film activated sludge membrane bioreactor and thus defeated the original purpose of GMBR development. The mass diffusion problem and sEPS production should be key areas of focus in future GMBR research.