This study was conducted using direct contact membrane distillation configuration for treating effluent from a thermophilic anaerobic membrane bioreactor. The effluent was taken as feed to better understand the effect of treating anaerobic wastewater (with and without biomass) on the flux and fouling interaction on membrane distillation in batch mode. While treating the effluent without biomass, permeate fluxes varied from 1.41 to 9.22 L/m² h at a temperature of (40–70 °C) and cross flow velocities of 0.005, 0.008, 0.01, 0.012 and 0.014 m/s. The COD and ammonia rejection at the stage was greater than 90%. In conditions where biomass was introduced in the feed at 6 and 12 g/L MLVSS, it was observed that permeate flux decreased from 2 to 0.6 L/m² h after 72 h operation at 12 g/L MLVSS wastewater, thus maximum observable fouling was also at 12 g/L. Fouling investigation concluded that the major foulant on the MD membrane surface was removable fouling, accounting for 71–77.5% of the total fouling at a loading rate of 6 and 12 g/L MLVSS, respectively. After cleaning, the membrane could recover 96% of the initial flux.