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Two synthetic approaches have been investigated for the surface modification of core–shell-shaped silica-coated magnetic nanoparticles with acid functions. A step procedure based on covalent attachment with diethylmalonate reagent and subsequent hydrolysis of the ester functions proved to be more efficient and versatile for the incorporation of such functionality than the one-pot method. The changes in surface morphology and chemical functionality were examined by X-ray diffraction, infrared spectroscopy, thermogravimetric analysis, zeta potential analysis, and transmission electron microscopy. The acid-functionalized Fe₃O₄@SiO₂ nanomaterial exhibited high adsorption affinity for the cationic dye methylene blue and, as such, is potentially of interest for wastewater treatment as an effective adsorbent for cationic dyes.