Nafion, an ion exchange polymer that is very resistant to chemical attack, even by strong oxidant at high temperatures, has found great increasing use as a film material; however, its use as immobilizing agent in third-generation biosensors is hindered due to the low rate of charge transfer in the pure Nafion film. In this work we showed that the use of functionalized multi-walled carbon nanotubes Nafion/MWCNTs composite film for modification of the carbon-based electrode surfaces would increase the charge transfer rate greatly; the composite has proven to efficiently immobilize two different heme proteins (catalase and cytochrome c) and to enhance the electrochemical performances of several carbon electrode materials (glassy carbon, mesoporous graphite, graphite and graphene) either used as classical electrodes or screen printed ones. The electrochemical signal of both redox proteins becomes more reversible and the electron transfer kinetic constant increases. At the same time the biological activity is maintained indicating that the immobilization procedure allows the proteins to retain a native-like structure.