Fouling in membrane contactors for recovery of dissolved methane (CH4) was investigated in this work. Two types of effluents from anaerobic membrane bioreactor (AnMBR) and upflow anaerobic sludge blanket (UASB) were tested under a continuous operational mode. Due to the higher fouling propensity of the UASB effluent, membrane fouling was more drastic, leading to a greater decline in the CH4 desorption flux with respect to the operational time. Also, the flux was observed to be influenced by the gas-liquid contact time and declined more severely with increasing liquid velocity. Membrane characterization revealed cake layer formation as the source of membrane fouling while foulants characterization indicated that the majority of the foulants were protein-like-substances with fluorescence spectra showing signals close to that of extracellular polymeric substances. On this basis, a mass transfer analysis was performed to understand the fouling resistance exerted by the cake layer and identify a parameter which best described the fouling mechanism. It was found that cake thickness can be used to express the change in fouling resistance in the case of the AnMBR effluent, while cake porosity was a better parameter in the case of the UASB effluent.