Biomimetically synthesized silica and conductive activated carbon nanofibers (CNFs) are used in a synergistic manner for the development of a novel electrochemical biosensor system. Poly(L-lysine) templated silica grows and encapsulates the CNF-immobilized enzyme generating a highly stabilizing nanostructured environment for the underlying protein. Concurrently, CNFs provide both the required surface area for the high-capacity enzyme immobilization required in biosensors as well as direct electron transfer to the inner platinum transducer. As a result, this silica/nanofiber superstructure is an ideal architecture for the development of electrochemical biosensor systems that can withstand exposure to extreme operational conditions, such as high temperatures or the presence of proteases. Acetylcholine esterase is used as the model catalyst and with the aid of spectroscopic data it is shown that the observed high operational stability of the biosensor is due to the direct interaction of the protein with the silica backbone, as well as due to the nanostructured enzyme confinement.