A novel method was proposed for the in situ synthesis of magnetite-containing mesoporous silica SBA-16 via a sol-gel process coupled with precipitation and oxidation. The effect of the added amounts of reactants on the mesostructural and magnetic properties of the magnetic mesoporous silica was investigated. It was determined that the synthesized magnetic mesoporous silica with a total pore volume of 0.64-0.96 cm3/g and an average pore diameter of 4.0-14.9 nm had a relatively high saturation magnetization value (1.11-5.77 emu/g) and a large surface area (258-747 m2/g). Lysozyme was chosen as a model protein to test the performance of the magnetic mesoporous silica as a protein adsorbent. The high adsorption capacity (up to 212 mg/g) suggested a promising future as bimolecular hosts for the magnetic mesoporous silica.