Biomedical applications ranging from tissue engineering to drug delivery systems require versatile biomaterials based on the scalable and tunable production of biopolymer nanofibers under physiological conditions. These requirements can be successfully met by a novel extrusion process through nanoporous aluminum oxide templates, which is presented in this study. With this simple method we are able to control the nanofiber diameter by chosing the size of the nanopores and the concentration of the biopolymer feed solution. Nanofiber assembly into different hierarchical fiber arrangements can be achieved with a wide variety of different proteins ranging from the intracellular proteins actin, α-actinin and myosin to the extracellular matrix components collagen, fibronectin, fibrinogen, elastin and laminin. The extrusion of nanofibers can even be applied to the polysaccharides hyaluronan, chitosan and chondroitin sulphate. Moreover, blends of different proteins or proteins and polysaccharides can be extruded into composite nanofibers. With these features our template-assisted extrusion process will lead to new avenues in the development of nanofibrous biomaterials.