It is one of the most important needs to develop renewable, scalable and multifunctional methods for the fabrication of 3D carbon architectures. Even though a lot of methods have been developed to create porous and mechanically stable 3D scaffolds, the fabrication and control over the synthesis of such architectures still remain a challenge. Here, we used Magnetospirillum magneticum (AMB-1) bacteria as a bio-template to fabricate light-weight 3D solid structure of carbon nanotubes (CNTs) with interconnected porosity. The resulting porous scaffold showed good mechanical stability and large surface area because of the excellent pore interconnection and high porosity. Steered molecular dynamics simulations were used to quantify the interactions between nanotubes and AMB-1 via the cell surface protein MSP-1 and flagellin. The 3D CNTs-AMB1 nanocomposite scaffold is further demonstrated as a potential substrate for electrodes in supercapacitor applications.