Gaining control over the nanoscale assembly of different electrode components in energy storage systems can open the door for design and fabrication of new electrode and device architectures that are not currently feasible. This work presents aqueous layer-by-layer (LbL) self-assembly as a route towards design and fabrication of advanced lithium-ion batteries (LIBs) with unprecedented control over the structure of the electrode at the nanoscale, and with possibilities for various new designs of batteries beyond the conventional planar systems. LbL self-assembly is a greener fabrication route utilizing aqueous dispersions that allow various Li+ intercalating materials assembled in complex 3D porous substrates. The spatial precision of positioning of the electrode components, including ion intercalating phase and electron-conducting phase, is down to nanometer resolution. This capable approach makes a lithium titanate anode delivering a specific capacity of 167 mAh g−1 at 0.1C and having comparable performances to conventional slurry-cast electrodes at current densities up to 100C. It also enables high flexibility in the design and fabrication of the electrodes where various advanced multilayered nanostructures can be tailored for optimal electrode performance by choosing cationic polyelectrolytes with different molecular sizes. A full-cell LIB with excellent mechanical resilience is built on porous insulating foams.