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In this research, a facile, two-step synthesis of FeO-L-graphene quantum dots (GQDs) nanocomposite is reported. This synthesis method comprises the preparation of GQDs via hydrothermal route, which should be conjugated to the L functionalized core-shell magnetic structure with the core of about 7.5-nm iron oxide nanoparticle and 3.5-nm L shell. L as a biocompatible natural amino acid, was used to link magnetite nanoparticles (MNPs) with GQDs. X-ray powder diffraction, Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray were used to investigate the presence and formation of MNPs, functionalized MNPs, and final hybrid nanostructure. Morphology and size distribution of nanoparticles were demonstrated by scanning electron microscopy and transmission electron microscopy. Finally, the magnetic and optical properties of the prepared nanocomposite were measured by vibrating sample magnetometer, ultraviolet-visible, and photoluminescence spectroscopy. The results show that FeO-L-GQDs nanocomposite exhibits a superparamagnetic behavior at room temperature with high saturation magnetization and low magnetic coercivity, which are 28.99 emu/g and 0.09 Oe, respectively. This nanocomposite also shows strong and stable emission at 460 nm and 530 nm when it is excited with the 235 nm wavelength. The magnetic GQDs structure also reveals the absorption wavelength at 270 nm. Therefore, FeO-L-GQDs nanocomposite can be considered as a potential multifunctional hybrid structure with magnetic and optical properties simultaneously. This nanocomposite can be used for a wide range of biomedical applications like magnetic resonance imaging (MRI) contrast agents, biosensors, photothermal therapy, and hyperthermia.