Saturation magnetization (Ms) of pristine bi-/tri-layered graphene (denoted as-FLG) is enhanced by over four (4) and thirty-four (34) times to 13.94 × 10-4 and 118.62 × 10-4 emu g-1, respectively, as compared to pristine FLGs (Ms of 3.47 × 10-4 emu g-1), via plasma-based-hydrogenation (known as graphone) and nitrogenation (known as N-graphene) reactions, respectively. However, upon organo-silane treatment on FLG (known as siliphene), the saturation magnetization is reduced by over thirty (30) times to 0.11 × 10-4 emu g-1, as compared to pristine FLG. Synchrotron based X-ray absorption near edge structure spectroscopy measurements have been carried out to investigate the electronic structure and the underlying mechanism responsible for the variation of magnetic properties. For graphone, the free spin available via the conversion of the sp2 → sp3 hybridized structure and the possibility of unpaired electrons from induced defects are the likely mechanism for ferromagnetic ordering. During nitrogenation, the Fermi level of FLGs is shifted upwards due to the formation of a graphitic like extra π-electron that makes the structure electron-rich, thereby, enhancing the magnetic coupling between magnetic moments. On the other hand, during the formation of siliphene, substitution of the C-atom in FLG by a Si-atom occurs and relaxes out the graphene plane to form Si-C tetrahedral sp3-bonding with a non-magnetic atomic arrangement showing no spin polarization phenomena and thereby reducing the magnetization. Thus, plasma functionalization offers a simple yet facile route to control the magnetic properties of the graphene systems and has potential implications for spintronic applications. © 2016 The Royal Society of Chemistry.