We present an in-depth examination of the composition and magnetism of cobalt (Co 2+ )-doped iron-oxide nanoparticles encapsulated in Pyrococcus furiosus ferritin shells. We show that the Co 2+ dopant ions were incorporated into the γ-Fe2O3/Fe3O4 core, with small paramagnetic-like clusters likely residing on the surface of the nanoparticle that were observed for all cobalt-doped samples. In addition, element-specific characterization using Mössbauer spectroscopy and polarized x-ray absorption indicated that Co 2+ was incorporated exclusively into the octahedral B-sites of the spinel-oxide nanoparticle. Comparable superparamagnetic blocking temperatures, coercivities, and effective anisotropies were obtained for 7, 10 and 12% cobalt-doped nanoparticles, and were only slightly reduced for 3% cobalt, indicating a strong effect of cobalt incorporation, with a lesser effect of cobalt content. Due to the regular particle size and separation that result from the use of the ferritin cage, a comparison of the effects of interparticle interactions on the disordered assembly of nanoparticles was also obtained that indicated significantly different behaviours between un-doped and cobalt-doped nanoparticles.