Surface derivatized magnetic nanoparticles have been commonly used for magnetic separation. Facile mechanisms are needed to be developed for the design of bio-functionalized magnetic hybrid materials, where the surfaces can be re-generated for the re-use of the developed platforms. Superparamagnetic iron oxide nanoparticles with a diameter below 10 nm were synthesized via a novel microwave-assisted hydrothermal method in the presence of citrate ions, which allowed to obtain uniform and negatively charged nanoparticles. These were then coupled with Poly-l-lysine (PLL), forming micrometer-sized self-assembled spherical entities. Cross-linking the PLL within these microspheres with glutaraldehyde stabilized them chemically and mechanically. The active bio-functionality was introduced by a protein grafting methodology, using m-maleimidobenzoyl-N-hydroxysulfosuccinimide ester (SMBS). The Moringa oleifera Coagulant Protein (MOCP) from a seed extract was employed for its characteristic coagulation activity. The performance of the MOCP functionalized microspheres was evaluated as a function of turbidity removal of problematic colloidal clay from water via magnetic separation, resulting in over 80% of activity within 15 min. Surface of these hybrid materials can be re-generated by treatment with alcohol, allowing their easy magnetic separation and re-use. The rapid and strong response with tunable magnetic property makes these hybrid microspheres a powerful tool for many potential applications, due to the general applicability of the developed methodology.