Multiphoton absorbing upconversion nanoparticles are emerging as bioimaging materials but are limited by the low quantum yield of their visible fluorescence. This article contains colloids of graphene quantum dots (GQDs), Neodymium, and Cobalt doped Graphene Quantum dots (Co-GQDs and Nd-GQDs) surrounded by carboxylic acids are synthesized which especially are suitable for bio applications; in this way, carboxylic acid groups exchanged by Amoxicillin as an antibiotic with bactericidal activity. The XRD diffraction method, TEM microscope, UV–Vis, and photoluminescence spectroscopies characterize the synthesized materials. The synthesized Quantum dots (QDs) exhibit upconversion properties and their emission is centered at 480 nm, but a red shift was observed with the increase of the excitation wavelength. In the emission spectra of synthesized QDs that can be related to the defect levels introduced by passivation of the QDs in the structure, the results show that with the interaction of the surface QDs with more carboxylic groups, the redshift is not observed. As the results indicate an increase in the intensity of upconversion emission is recorded for Co-GQDs and Nd-GQDs. The absolute quantum efficiency (QY) for Co-GQDs and Nd-GQDs were determined to be 41% and 100% more than GQDs respectively. DFT calculations indicate a strong bond between graphene and cobalt and Neodymium atoms. In doped materials, there are trap levels between the band gap of the GQDs which are responsible for increasing the intensity of the upconversion phenomenon.