To fabricate metal nanocrystal (NC) memories based on iron ferritin proteins, we propose a method for embedding ferritin cores in SiO2 and performing a reduction process by rapid thermal annealing (RTA) in a hydrogen atmosphere. An iron oxide core biochemically synthesized by ferritin was used to fabricate a high-density memory node array of 7.7 × 1011 dots/cm2. Reduction intermediates and metallic iron NCs were obtained in a short time by using a hydrogen atmosphere RTA with the iron oxide core embedded in SiO2. Metal-oxide-semiconductor memory structures were fabricated, capacitance–voltage (C–V) measurements were performed, and hysteresis (memory window) suggesting charging and discharging of NCs was observed. Furthermore, the memory window and the charge injection threshold tended to vary depending on the reduction temperature. Since these values are proportional to the magnitude of the dot work function (or electron affinity), it is assumed that the formation of reduced intermediates NCs with varying work functions depending on the treatment temperature affects the electrical properties. The results suggest that the work function of the charge retention node can be controlled by reducing the metal oxide, enabling a new approach to memory design that actively employs the reduction process.