A fully starch-derived bioactive 3D porous scaffold is developed. The bioactivity is introduced through nanosized graphene oxide (nGO) derived from starch by microwave-assisted degradation to carbon spheres and further oxidation to GO nanodots. nGO is covalently attached to starch to prepare functionalized starch (SNGO) via an esterification reaction. nGO and SNGO exhibit no cytotoxicity to MG63 at least up to 1000 µg mL under (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. Porous scaffolds consisting of starch and SNGO (S/SNGO) or nGO (S/nGO) are prepared by freeze drying. The porosity and water uptake ability of the scaffolds depend on the concentration of nGO. Moreover, nGO, as a bioactive nanofiller, functions as an effective anchoring site for inducing CaP recrystallization in simulated body fluid. Among all modified starch-based scaffolds, the S/SNGO scaffold containing the highest concentration of covalently attached SNGO (50%) induces the largest amount of hydroxyapatite, a type of CaP crystal that is closest to bone. The prepared 3D porous nGO functionalized scaffold, thus, exhibits potential promise for bone/cartilage tissue engineering.