The structure of silk elastin-like protein (SELP) block copolymers containing Fe3O4 magnetic nanoparticles are investigated. These materials have potential applications for hyperthermia cancer therapy. SELPs undergo a gel transition at physiological temperatures, which can be used to localize delivery of nanoparticles at tumor sites. Vibrating sample magnetometry (VSM), transmission electron microscopy (TEM), and small angle neutron scattering (SANS) are used to characterize the nanoparticles and the SELP-nanoparticle nanocomposite system. A series of nanoparticles with three different nominal diameters, 30, 50 and 80 nm, were added to 4 and 8 wt.% SELP samples. Different functionalities on the nanoparticle surface affect their interactions with SELP. The 50 nm nanoparticles in SELP exhibit chaining (linear association of the nanoparticles), while the 30 nm nanoparticles are too small and settle out of the polymer mesh and the 80 nm nanoparticles tend to cluster without any regard for SELP structure. The SELP concentration does not have a major affect on nanoparticle behavior in the nanocomposites.