The surface of a glass plate was molecularly engineered to become antimicrobial by coating it with a self-assembled layer of (3-aminopropyl) trimethoxysilane (APTMS) and then with an overlayer of antimicrobial benzyldodecyldimethylammonium bromide (BAB). Hyperthermal H2 molecules with a kinetic energy of about 15 eV were used as “bullets” to collide with BAB and APTMS to selectively cleave the CH bonds in them. Subsequent recombination of the carbon radicals thus formed lead to the crosslinking and fixation of BAB to APTMS which is itself strongly bonded to the glass surface via silanization. Molecular dynamics simulations were conducted to validate this peculiar hyperthermal hydrogen induced cross-linking (HHIC) mechanism, and hyperthermal hydrogen molecules with a high flux density over 1 × 1015 H2/cm2s for completing the HHIC process in 10 s in reaction-time were experimentally generated with a specifically designed instrument. The glass silanization with APTMS and the fixation of BAB molecules were assessed and confirmed by water contact angle (WCA) measurements, X-ray photoelectron spectroscopy (XPS), as well as atomic force microscopy (AFM). The antimicrobial activity against staphylococcus aureus was confirmed with the standard ISO/DIS 22196 test-method.