This study proposes new kinds of functionalization procedures able to preserve specific properties of carbon nanotubes (CNTs) and to improve compatibility with the epoxy matrix. Through a covalent approach, for the first time, CNTs are functionalized with the same hardener agent, 4,4′-diaminodiphenyl sulfone, employed to solidify the epoxy matrix and capable to fulfill mechanical requirements of industrial structural resins. The same CNTs are non-covalently modified through the polymer wrapping mechanism with benzoxazine (Bz) terminated polydimethylsiloxane (PDMS). The comparison between electrical and mechanical properties of the nanocomposites highlights the success of the non-covalent functionalization in determining an increase in the glass transition temperature (Tg) and in better preserving the unfunctionalized CNT electrical conductivity. Besides, tunneling atomic force microscopy (TUNA), powerful to catch ultra-low currents, has been used for revealing the morphology on nanoscale domains and detecting the conductivity on the same location of CNT/epoxy resins. No electrical contacts to the grounds have been used for the TUNA analysis; a procedure that does not alter the results on the interface domains which experience contact areas with strong differences in their properties. The effectiveness of performed CNT functionalizations as a route to impart self-healing efficiency to the resin formulations has also been proved.