Anaerobic membrane bioreactors (AnMBRs) have demonstrated an excellent capability to treat domestic wastewater. However, biofouling reduces membrane permeability, increasing operational costs and overall energy demand. Soluble microbial products (SMPs) that build up on the membrane surface play a significant role in the biofouling. In this study, the production of SMPs in a 32 L submerged AnMBR operated at three different organic loads (3.0, 4.1 and 1.2 kg chemical oxygen demand (COD)/m3d for phases 1, 2 and 3, respectively) during long-term operation of the reactor (144, 83 and 94 days) were evaluated. The samples were taken from both the permeate and the sludge at three different heights (0.14, 0.44 and 0.75 m). Higher production of SMPs was obtained in phase 2, which was proportional to the membrane fouling. There were no statistically significant differences (p > 0.05) in the SMPs extracted from sludge at different heights among the three phases. In the permeate of phases 1, 2 and 3, the membrane allowed the removal of 56%, 70% and 64% of the SMP concentration in the sludge. SMPs were characterized by molecular weight (MW). A bimodal behavior was obtained, where fractions prevailed with an MW < 1 kDa, associated with SMPs as utilization-associated products (UAPs) caused fouling by the pore-blocking mechanism. The chemical analysis found that, in the SMPs, the unknown COD predominated over the known COD, such as carbohydrates and proteins. These results suggest that further studies in SMP characterization should focus on the unknown COD fraction to understand the membrane fouling in AnMBR systems better.