A magnetic mesoporous silica, Fe3O4@SiO2@KCC-1 (MMS), was prepared using a hydrothermal method and subsequently modified by post-grafting to synthesize Fe3O4@SiO2@KCC-1-SH (MMS-SH). The synthesized mesoporous materials were characterized using various techniques, including X-ray diffraction (XRD), vibrating sample magnetometry (VSM), field emission scanning electron microscopy (FE-SEM), X-ray energy diffraction spectroscopy (EDS) analysis and mapping, nitrogen adsorption/desorption measurement, Thermal gravimetric analysis (TGA) and Fourier transform infrared (FT-IR) spectroscopy. Their removal capacity for heavy metal ions was determined with flame atomic absorption spectroscopy (AAS). Due to their large surface area, these adsorbents were used for the removal of Cu(II), Ni(II), Cd(II), Hg(II), and Pb(II) ions. The unmodified MMS exhibited removal capacities of 24.10, 28.54, 21.71, 32.5, and 30.06 mg/g for Cu(II), Ni(II), Cd(II), Hg(II), and Pb(II) ions, respectively. The removal of heavy metal ions by MMS followed a pseudo-first-order kinetic model and fit well with the Langmuir model. However, modifying the surface of the MMS with thiol groups significantly increased the removal capacity for all mentioned metal ions to 36.21, 32.83, 27.34, 48.75, and 41.40 mg/g, respectively. The removal of heavy metal ions by MMS-SH followed a pseudo-second-order kinetic model and fit well with the Temkin model. The antibacterial assays showed that the synthesized mesoporous materials were generally more effective against both planktonic Escherichia coli (gram-negative bacterium) and its ability to form biofilm compared to Staphylococcus aureus (gram-positive bacterium).