The characteristics of foulant in the cake layer and bulk suspended solids of a 10 L submerged anaerobic membrane bioreactor (AnMBR) used for treatment of palm oil mill effluent (POME) were investigated in this study. Three different organic loading rates (OLRs) were applied with prolonged sludge retention time throughout a long operation time (270 days). The organic foulant was characterized by biomass concentration and concentration of extracellular polymeric substances (EPS). The thicknesses of the cake layer and foulant were analyzed by confocal laser scanning microscopy and Fourier transform infrared spectroscopy. The membrane morphology and inorganic elements were analyzed by field emission scanning electron microscope coupled with energy dispersive X-ray spectrometer. Roughness of membrane was analyzed by atomic force microscopy. The results showed that the formation and accumulation of protein EPS in the cake layer was the key contributor to most of the fouling. The transmembrane pressure evolution showed that attachment, adsorption, and entrapment of protein EPS occurred in the membrane pores. In addition, the hydrophilic charge of proteins and polysaccharides influenced the adsorption mechanism. The composition of the feed (including hydroxyl group and fatty acid compounds) and microbial metabolic products (protein) significantly affected membrane fouling in the high-rate operation.