Finding an effective and excellent pertinent single catalyst material for multipurpose application for the purification of hydrocarbons in fuels (desulfurization), and for efficient removal of heavy metals from industrial effluent is greatly endowed. In the present work, a hybrid nanocomposite of ultrafine magnetite (Fe3O4) nanoparticle embedded on the surface of in-situ nitrogen doped layered GO (NGO) sheets were fabricated by sol-gel method and treatment with microwave irradiation technique is reported for the first time. The results show a high removal efficiency of 97 % for multiple heavy metals (Pb2+, Cd2+, Cu2+, Cr+2, Mn+2etc.) in industrial effluent and as well as in synthetic water with a very good retention performance of 99 %. The composites were tested against the elimination of sulfur from thiophene is 1.495 mmol g−1 is reported high is due to coupling and coordination of nitrogen with FeO and C. Recycling studies showed that the developed composites had excellent recyclability, with <82 % removal at the 5th cycle; its feasibility was evaluated using industrial effluent water and in synthetic water. Surface phenomena studies presented here revealed that the adsorptive removal processes of heavy metals involved π electron donor-acceptor interactions, ion exchange, and electrostatic interactions, along with surface complexation that showed an excellent synergism. A high stability, and retention performance is better than the pure Fe3O4 and NGO sheets. We hope that this study will motivate and give further scope for scientists working on magnetite-based graphene nanocomposites.