Pd nanoparticles exhibiting permanent magnetism at room temperature have been prepared within the apoferritin cavity. Pd nanoparticles in air and under an inert atmosphere were synthesized to study the influence of the aerobic and anaerobic conditions in the final magnetic properties. The surface of nanoparticles as well as the type of crystalline phase could determine the magnetic properties. X-ray powder diffraction, including Debye-function analysis, transmission electronic microscopy, and magnetization measurements have been used for characterizing the nanoparticles.