Mono and bimetallic modified MCM-41(Mobil Composition of Matter No. 41): Zn-MCM (ZM), Zn/Co-MCM41 (ZCM), and Zn/Pd-MCM-41 (ZPM) molecular sieves were produced by a surfactant-assisted technique. The structural and textural features were examined through spectroscopic and analytical techniques. The XRD analysis indicated broadening of diffraction peaks and a shift towards higher 2-theta values in the metal-incorporated (M-MCM-41) samples, confirming the successful integration of metal atoms into the MCM-41 framework; it also highlighted the preservation of a hexagonal structure with reasonable regularity, emphasizing the influence of metal incorporation on the mesoporous architecture of MCM-41. N2 adsorption–desorption isotherms revealed type IV isotherms for all samples; the BET specific surface area decreased to 672.48, 667.90, and 562.50 m2/g in ZM, ZCM, and ZPM, respectively comparing to the unincorporated MCM-41 sample (1200 m2/g), indicating partial filling of mesopores by metal centers, as confirmed by TEM images. The diffuse reflectance spectra exhibited a noteworthy optical band gap reduction of MCM-41 (5.98 eV) upon the incorporation of Zn and Co/Zn ions, resulting in values of 5.86 and 5.24 eV, respectively, with refractive index values close to 2. Additional absorption bands energies are observed at 3.14, 3.18, and 1.70 eV in ZM, ZPM, and ZCM samples, respectively suggesting the suitability of the metal incorporated samples for the photocatalytic applications. The M-incorporated samples exhibited a decline in the transmission intensity accompanied by small shifts. The enhanced antimicrobial activity of the metal-incorporated samples, surpassing that of the pure MCM-41 against a variety of tested microorganisms, is attributed to the presence of incorporated metal species, which create a more acidic environment and substantially contribute to the heightened antimicrobial effectiveness. The ZM compound demonstrated potent inhibition against Bacillus cereus and Pseudomonas aeruginosa bacteria, displaying comparable efficacy to Ampicillin, as a reference antibiotic. Additionally, ZPM exhibited considerable inhibitory activity against Escherichia coli, surpassing the reference antibiotic and showing similar effectiveness against Bacillus cereus, Pseudomonas aeruginosa, and Salmonella typhimurium.