This investigation involved synthesizing a nanocomposite heterostructure, Chitosan-MgO-SiO2@aminosilane, using the physical blending of chitosan-MgO-silica with aminosilane using the sol–gel technique. The prepared nanocomposites were characterized using x-ray diffraction (XRD), Scanning/Transmission Electron Microscope (SEM-EDX/TEM), Fourier Transform Infrared Spectroscopy (FTIR), and optical analysis to investigate the microstructural and spectroscopic properties. XRD results confirmed the formation of orthorhombic Mg2SiO4 within the fabricated system. FTIR analysis verified interactions among chitosan, MgO-silica, and aminosilane, leading to the development of diverse functional groups, including M-O bonds, silanol-hydroxyl ions, and heteropolymeric-O-M within the chitosan-MgO-SiO2@aminosilane nanocomposite. Optical studies demonstrated that aminosilane-incorporated samples have two distinct absorption bands around 215 nm and 419 nm, corresponding to the electronic transitions π–π* (k-band) and n–π* (R-band), respectively. The absorption band at 400 nm is ascribed to localized surface plasmon resonance (SPR). The incorporation of aminosilane resulted in a decrease in the direct transition energy gap from 2.677 to 2.399 eV. The nanocomposites displayed significant antimicrobial activity against pathogenic microorganisms such as Gram-positive Staphylococcus aureus, Gram-negative Pseudomonas aeruginosa, and pathogenic fungi Candida albicans and Aspergillus niger. The positive antimicrobial response of the fabricated nanocomposites candidates them for various applications, including wound dressings and food packaging.