The growing threat posed by microorganisms has prompted us to conduct research into a new type of material that could serve as an alternative to currently used disinfectants and antibiotics. The aim of the research was to develop an antibacterial surface based on a mesoporous silica structure containing copper phosphonate functional groups responsible for generating reactive oxygen species (ROS). The presented research includes an in-depth characterisation of the developed material, with particular emphasis on the influence of the molecular structure on the ability to generate ROS. The analysis of the vibrational spectroscopy results was supported by numerical simulations, which confirmed the involvement of copper phosphonate groups in the formation of ROS. Direct evidence of the presence of ROS inside the silica structure was also confirmed by fluorescence microscopy. Next, the effect of ROS generated by the prepared surfaces on healthy human epidermal cells and pathogenic microorganisms was presented. The antibacterial properties were tested on a wide range of bacteria, both Gram-negative and Gram-positive, including drug-resistant ones, as well as on fungi. In the case of the tested surface, an additional effect was obtained due to the structure of the SBA-15 silica grains forming the morphology of the coating, which significantly influences biofilm formation. This allowed for a synergistic effect of surface morphology and the presence of ROS, resulting in high antibacterial activity while maintaining low cytotoxicity towards healthy human cells.