Iron oxide nanoparticles mineralized within the internal cavity of Ferritin protein cage are extremely appealing for the realization of multifunctional therapeutic and diagnostic agents for cancer treatment by drug delivery, magnetic fluid hyperthermia (MFH) and magnetic resonance imaging. Being the maximum mean size imposed by the internal diameter of the protein shell (ca. 8 nm) too small for the use of these systems in MFH, a valuable strategy for the improvement of the hyperthermic efficiency is increasing the magnetic anisotropy by doping the iron oxide with divalent Co ions. This strategy has been demonstrated to be highly efficient in the case of iron oxide nanoparticles mineralized in Human Ferritin (HFt). However, a deterioration of nanoparticles crystallinity and consequently a reduction of the hyperthermic efficiency were observed with increasing Co-doping. In this contribution, we compare two series of Co-doped iron oxide nanoparticles (Co-doping level up to 15%) mineralized into HFt and into Ferritin from the archaea Pirococcus Furiosus (PfFt), the protein structure of which differs for the nucleation sites, with the aim of increasing the crystalline quality of the inorganic cores for larger Co doping. Highly monodisperse nanoparticles of 6-7 nm were obtained in both series. The structural and magnetic characterization indicate that the PfFt series is less subjected to crystallinity deterioration with increasing Co content with respect to the HFt one. Such difference is reflected in the hyperthermic efficiency, which reaches the maximum value for different intermediate Co-doping (10% and 5% for PfFt and HFt, respectively), and goes to zero for further Co-doping increments.