The high efficiency of using N-(phosphonomethyl)iminodiacetic acid (PMIDA) as a surfactant for formation of a silica coating on Fe₃O₄ magnetic nanoparticles (MNPs) with a large surface area has been demonstrated. The coating of PMIDA-stabilized MNPs with silica and their further APS-functionalization significantly increased the specific area (up to 203 m² g⁻¹) and the number of amino groups (up to 1.12 mmol/g) grafted on their surface compared to nanomaterials synthesized without preliminary SiO₂-coating. The comparative study of the peptide modification efficiency, using as an example pH-low insertion peptide (pHLIP), of MNPs coated with 3-aminopropylsilane (APS) or SiO₂/APS was carried out. It has been shown that silica coating of PMIDA-stabilized MNPs leads to a significant increase in the degree of immobilization of the peptide (up to 22 μmol per g of MNPs). Comprehensive characterization of the obtained materials at each stage of the synthesis was carried out using scanning electron microscopy (SEM), energy dispersive X-ray fluorescence spectroscopy (EDX), BET analysis, ATR Fourier transformed infrared spectroscopy (FTIR), termogravimetric analysis (TGA), CHN-elemental analysis, dynamic light scattering (DLS), and vibrating sample magnetometry (VSM). The proposed approach to applying SiO₂-coating of MNPs can be useful for design of new materials for biomedical and chemical purposes.