In this research, two novel nano-size inorganic-bioorganic hybrids based on graphene oxide were prepared via a two-step process. The ionic liquids obtained through the reaction of arginine and malonic acid, in a 1:1 and 1:2 molar ratio, afford mono-Arg malonate and di-Arg malonate, respectively. These two bio-based ILs characterized via FT-IR, 1H-NMR, 13C-NMR, and GC-MASS techniques. In the second part, they embedded on graphene oxide core to gain the final nano-size inorganic-bioorganic hybrids (GO@mono-Arg malonate and GO@di-Arg malonate), which were identified through, FT-IR, FESEM, EDAX, and TGA/DSC, analysis. The catalytic efficacy of two obtained nanostructures examined in the synthesis a wide range of spiro[indeno[1,2-d]pyrimidineindoline]ones, spiro[indoline-pyrimido[4,5-d]pyrimidine]ones, and dihydro-spiro[indoline-pyrimidine]-carboxylates via the reaction of 1,3-cyclic/linear dicarbonyls (1,3-indanedione, barbituric acid, Meldrum’s acid, ethyl acetoacetate, and 4-hydroxycoumarin), heterocyclic 1,2-dicarbonyls (isatin, 5-chloroisatin, 5-bromoisatin, acenaphthenequinone, and ninhydrin), and urea/thiourea/guanidine under solvent-free conditions at 80 °C. The results affirmed that the GO@di-Arg malonate accelerated the reactions faster than GO@mono-Arg malonate. The recovery and reusability of the GO@di-Arg malonate was examined within two cycles successfully. The recovered GO@di-Arg malonate was determined by FESEM analysis.