The biotransformation of rice husk ash (RHA) by Fusarium oxysporum to generate silica nanoparticles was carried out using two different commercial growth media: malt-glucose (MG) and malt-glucose-yeast-peptone (MGYP). Biomass production, substrate consumption, organic acids production, and solubilized silica were measured during RHA biotransformation. Extracellular proteins were analyzed by SD-PAGE. Silica nanoparticles were analyzed by XRD, zeta potential, SEM, and TEM. The results showed that the production of organic acids was not directly related to the solubilization of silica. Solubilization and stabilization of silica occur mainly in the exponential growth phase of F. oxysporum, which are associated with the action of extracellular proteins with sizes 24, 55, and 70 kDa. MG medium presented the best performance for the growth of F. oxysporum and production of semicrystalline, quasi-spherical silica nanoparticles in the range of 2–8 nm.