The presence of siloxanes poses a significant threat to membrane integrity, particularly during the purification of biogas at ambient temperatures. Their elevated molecular weight and chemical affinity for specific organic compounds result in their adsorption onto the membrane surfaces. To facilitate membrane recovery, the temperature may be raised, provided it remains within the manufacturer's specified limits. This process is typically enhanced by an overnight wash with nitrogen gas or the application of a vacuum to promote desorption.

Aside from membrane fouling issues from the raw biogas such as by siloxanes and colloids as well as from metal dust particles resulting from gas compression, the major membrane challenges in biogas purification are accelerated aging and plasticization due to the high differential pressures required for separating gas molecules.