The use of carbon fiber reinforced polymers (CFRP) as multifunctional structural supercapacitors has been limited by the low ionic conductivity and/or mechanical properties of the insulator separator. Here we propose a novel type of “structural separator” based on aligned insulating nanowires “nanostitched” between carbon microfiber laminates. Proof-of-concept composites were fabricated using aligned alumina nanotubes (ANTs) as well as standard commercial separators between carbon CF prepregs. ANTs nanostitched-composite laminates showed similar mechanical properties as the structural composite with no separator, while the commercial separator exhibited reduced strength due to interface failure. ANTs embedded in polymer electrolyte revealed 2X higher ionic conductivity than the pure electroactive polymer due to the nanowires disrupting the polymer semi-crystallinity. This new structural separator architecture allows standard CFRP structural composites to act as a multifunctional energy storage device, with the potential to enhance energy storage capabilities due to the process-structure coupling in ionically-conductive polymer.