A combined surface treatment (i.e., surface grafting and a layer-by-layer (LbL) approach) is presented to create advanced biomaterials, i.e., 3D poly(l-lactide) (PLLA) microsphere scaffolds, at room temperature. The grafted surface plays a crucial role in assembling polyelectrolyte multilayers (PEMs) onto the surface of the microspheres, thus improving the physicochemical properties of the 3D microsphere scaffolds. The grafted surface of the PLLA microspheres demonstrates much better PEM adsorption, improved surface coverage at low pH, and smoother surfaces at high pH compared with those of nongrafted surfaces of PLLA microspheres during the assembly of PEMs. They induce more swelling than nongrafted surfaces after the assembly of the PEMs and exhibit blue emission after functionalization of the microsphere surface with a fluorescent dye molecule. The 3D scaffolds functionalized with and without nanosheets not only exhibit good mechanical performance similar to the compressive modulus of cancellous bone but also exhibit the porosity required for cancellous bone regeneration. The magnetic nanoparticle-functionalized 3D scaffolds result in an electrical conductivity in the high range of semiconducting materials (i.e., 1-250 S cm-1). Thus, these 3D microsphere scaffolds fabricated by surface grafting and the LbL approach are promising candidates for bone tissue engineering.