In this letter, we report on the high frequency (239.2 and 336 GHz) electron spin resonance (ESR) studies performed on graphene quantum dots (GQDs), prepared through a wet chemistry route from three types of coal: (a) bituminous, (b) anthracite, and (c) coke; and from non-coal derived GQDs. The microwave frequency-, power-, and temperature-dependent ESR spectra coupled with computer-aided simulations reveal four distinct magnetic defect centers. In bituminous- and anthracite-derived GQDs, we have identified two of them as intrinsic carbon-centered magnetic defect centers (a broad signal of peak to peak width = 697 (10−4 T), g = 2.0023; and a narrow signal of peak to peak width = 60 (10−4 T), g = 2.003). The third defect center is Mn2+ (6S5/2, 3d5) (signal width = 61 (10−4 T), g = 2.0023, Aiso = 93(10−4 T)), and the fourth defect is identified as Cu2+ (2D5/2, 3d9) (g⊥ = 2.048 and g‖ = 2.279), previously undetected. Coke-derived and non-coal derived GQDs show Mn2+ and two-carbon related signals, and no Cu2+ signal. The extrinsic impurities most likely originate from the starting coal. Furthermore, Raman, photoluminescence, and ESR measurements detected no noticeable changes in the properties of the bituminous GQDs after one year. This study highlights the importance of employing high frequency ESR spectroscopy in identifying the (magnetic) defects, which are roadblocks for spin relaxation times of graphene-based materials. These defects would not have been possible to probe by other spin transport measurements.