Iron oxide nanoparticles are known to be used for their exorbitant properties in a multitude of fields. It has huge applications in mining industries, biomedicine, wastewater treatment, protein purification, food processing and much more. In the present study, researchers tried to unfold the understanding of iron oxide nanoparticles structuring using spray drying method. The study showed the formation of micrometer size aggregates having magnetic property comparable to that of individual nanoparticles. Besides this, researchers found that the superparamagnetic property of the multicore structure formed was not lost. The changes in the aggregates through the addition of silica-based nanoparticles in the suspension showed significant control of the resulting magnetization by altering the iron oxide content. Interestingly, it was observed that the changes in silica content to only 20% brought significant alteration in the morphology of iron oxide nanoparticles. Wherein the inflated like shape of the pure iron oxide nanoparticles was observed to be converted into a spherical structure. These aggregates with different magnetization can be separated in a column under the influence of the magnetic field provided by an attached permanent magnet. These iron oxide aggregates are coupled with a ligand containing nitrilotriacetic acid (NTA) groups that can be used to purify 6-histidine tagged proteins. The present studies show the purification of protein A using this mechanism. The major benefit of this new purification system under the influence magnetic field is the high degree of recyclability. The system can be used effectively without losing much protein.