We have developed a simple and effective strategy to prepare an enzymatic membrane by the admixing of a halloysite clay nanotube–lipase complex and a chitosan solution. The loading of 3 wt% lipase into the lumen of halloysite clay nanotubes was enhanced with an electrostatic interaction. 10 wt% of lipase–nanotubes were dispersed in an aqueous chitosan solution and cast as a coating. The enzymatic chitosan–halloysite membranes displayed increased pH, temperature stability and long-term usability for the catalytic decomposition of lipids: 90% of the initial activity was preserved at 80 °C, 70% of the functionality remained at the high pH of 9, and 85% of the activity was sustained after ten continuous cycles of use. The placement of the second antimicrobial enzyme–lysozyme at the outer surface of the clay nanotubes allowed for a synergistic increase in the activity of the composite antibacterial formulation. The lipase/lysozyme-co-immobilized clay nanotube–chitosan membranes are promising in anti-biofouling applications.