Iron oxide nanoparticles were microencapsulated using fibroin, a protein polymer of silk fiber, for theragnostic applications. The content of iron oxide was determined to be 4.28% by thermogravimetric analysis and 5.11% by magnetometer. A suspension of murine fibroblast 3T3 cells grown in medium supplemented with iron oxide-microcapsules turned clear in response to the magnetic force and the cells aggregated to the magnet direction. Neodymium magnets placed on the top of the culture dish, and attracted cells to the center of the culture surface. The cells collected on the culture surface aggregated to form a rough spheroid of 2 mm in a diameter after 72 h. In the outer layer of the cell aggregate, cells were relatively large and gathered together to form a dense tissue, but the central part was observed to undergo cell death due to the mass transfer restriction. In the outer layer, iron oxide-microcapsules were lined up like chains in the direction of magnetic force. Using microCT, it was demonstrated that the iron oxides inside the cell aggregate were not evenly distributed but biased to the magnetic direction.