We have fabricated biocompatible nanofiber hydrogels with diverse sizes of ferritin clusters according to the mixing temperature of solutions employing electrospinning. Poly(vinyl alcohol) (PVA) was used as a polymeric matrix for fabricating nanocomposites. By thermal means we controlled the interaction between the host PVA hydrogel and the protein shell on ferritin bionanoparticles to vary the size and concentration of ferritin clusters. The clustering of ferritin was based on the partial unfolding of a protein shell of ferritin. By studying the magnetic properties of the PVA/ferritin nanofibers according to the mixing temperature of the PVA/ferritin solutions, we confirmed that the clustering process of the ferritin was related to changes in the superparamagnetic properties and magnetic resonance imaging (MRI) contrast of the PVA/ferritin nanofibers. PVA/ferritin nanofiber hydrogels with diverse spatial distributions of ferritin nanoparticles are applicable as MRI-based noninvasive detectable cell culture scaffolds and as artificial muscles because of their improved superparamagnetic properties.