Biofouling is the main challenge in the operation of anaerobic membrane bioreactors (AnMBRs). Biofouling strongly depends on temperature; therefore, we hypothesize that the interactions and viscoelastic properties of soluble microbial products (SMP) and extracellular polymeric substances (EPS) vary with temperature, consequently influencing membrane permeability. This study compares the performance of an AnMBR operated at a similar permeate flux at two temperatures. The transmembrane pressure (TMP) rose rapidly after 5 ± 2 days at 25 °C but only after 18 ± 2 days at 35 °C, although the reactor's biological performance was similar at both temperatures, in terms of the efficiency of dissolved organic carbon removal and biogas composition, which were obtained by changing the hydraulic retention time. Using confocal laser scanning microscopy (CLSM), a higher biofilm amount was detected at 25 °C than at 35 °C, while quartz crystal microbalance with dissipation (QCM-D) showed a more adhesive, but less viscous and elastic EPS layer. In situ optical coherence tomography (OCT) of an ultra-filtration membrane, fed with the mixed liquor suspended solids (MLSS) at the two temperatures, revealed that while a higher rate of TMP increase was obtained at 25 °C, the attachment of biomass from MLSS was markedly less. Increased EPS adhesion to the membrane can accelerate TMP increase during the operation of both the AnMBR and the OCT filtration cell. EPS's reduced viscoelasticity at 25 °C suggests reduced floc integrity and possible increased EPS penetration into the membrane pores. Analysis of the structures of the microbial communities constituting the AnMBR flocs and membrane biofilms reveals temperature's effects on microbial richness, diversity, and abundance, which likely influence the observed EPS properties and consequent AnMBR fouling.